Starting phenix.real_space_refine on Wed Mar 4 22:48:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qn6_14068/03_2026/7qn6_14068.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qn6_14068/03_2026/7qn6_14068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qn6_14068/03_2026/7qn6_14068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qn6_14068/03_2026/7qn6_14068.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qn6_14068/03_2026/7qn6_14068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qn6_14068/03_2026/7qn6_14068.map" } resolution = 2.9 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: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 10941 2.51 5 N 2701 2.21 5 O 3087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s 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: 16821 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2749 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2683 Chain: "B" Number of atoms: 2764 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2664 Chain: "C" Number of atoms: 2765 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2663 Chain: "D" Number of atoms: 2716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2721 Chain: "E" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2592 Classifications: {'peptide': 324} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 310} Chain breaks: 1 Chain: "K" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "L" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "M" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" 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: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" 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: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'EPE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'EPE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'EPE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 13 residue: pdb=" N AASN A 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 41 " occ=0.50 residue: pdb=" N ALEU A 125 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 125 " occ=0.50 residue: pdb=" N ASER A 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 209 " occ=0.50 residue: pdb=" N ALEU A 214 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 214 " occ=0.50 residue: pdb=" N AASN B 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN B 41 " occ=0.50 residue: pdb=" N ASER B 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 209 " occ=0.50 residue: pdb=" N ALEU B 214 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU B 214 " occ=0.50 residue: pdb=" N ASER B 229 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 229 " occ=0.50 residue: pdb=" N AASN C 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C 41 " occ=0.50 residue: pdb=" N ATYR C 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 66 " occ=0.50 residue: pdb=" N ALEU C 125 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU C 125 " occ=0.50 residue: pdb=" N ASER C 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 209 " occ=0.50 residue: pdb=" N ASER D 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER D 209 " occ=0.50 Time building chain proxies: 5.67, per 1000 atoms: 0.34 Number of scatterers: 16821 At special positions: 0 Unit cell: (118.272, 135.296, 124.544, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 3087 8.00 N 2701 7.00 C 10941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 164 " - pdb=" SG CYS E 178 " distance=2.03 Simple disulfide: pdb=" SG CYS K 409 " - pdb=" SG CYS K 483 " distance=2.03 Simple disulfide: pdb=" SG CYS L 409 " - pdb=" SG CYS L 483 " distance=2.03 Simple disulfide: pdb=" SG CYS M 409 " - pdb=" SG CYS M 483 " distance=2.03 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=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG E 501 " - " ASN E 103 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 149 " " NAG H 1 " - " ASN C 149 " " NAG I 1 " - " ASN D 149 " " NAG a 1 " - " ASN A 80 " " NAG b 1 " - " ASN B 80 " " NAG c 1 " - " ASN C 80 " " NAG d 1 " - " ASN D 80 " Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 1.0 seconds 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3816 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 24 sheets defined 35.2% alpha, 40.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 84 through 91 removed outlier: 3.501A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 218 through 225 removed outlier: 3.571A pdb=" N LEU A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.679A pdb=" N VAL A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 242 Processing helix chain 'A' and resid 246 through 271 removed outlier: 3.733A pdb=" N THR A 271 " --> pdb=" O HIS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 307 Processing helix chain 'A' and resid 423 through 446 removed outlier: 3.525A pdb=" N ILE A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Proline residue: A 432 - end of helix Processing helix chain 'B' and resid 8 through 21 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.500A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 218 through 225 removed outlier: 3.572A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 242 removed outlier: 3.678A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 271 removed outlier: 3.732A pdb=" N THR B 271 " --> pdb=" O HIS B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 307 Processing helix chain 'B' and resid 423 through 446 removed outlier: 3.525A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 84 through 91 removed outlier: 3.501A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 218 through 225 removed outlier: 3.572A pdb=" N LEU C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 242 removed outlier: 3.678A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 242 " --> pdb=" O VAL C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 271 removed outlier: 3.733A pdb=" N THR C 271 " --> pdb=" O HIS C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 307 Processing helix chain 'C' and resid 423 through 446 removed outlier: 3.524A pdb=" N ILE C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'D' and resid 8 through 21 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 84 through 91 removed outlier: 3.500A pdb=" N ASP D 89 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 177 through 181 Processing helix chain 'D' and resid 218 through 225 removed outlier: 3.570A pdb=" N LEU D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 242 removed outlier: 3.678A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 271 removed outlier: 3.732A pdb=" N THR D 271 " --> pdb=" O HIS D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 307 Processing helix chain 'D' and resid 423 through 446 removed outlier: 3.524A pdb=" N ILE D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 42 through 50 Processing helix chain 'E' and resid 98 through 101 Processing helix chain 'E' and resid 112 through 119 removed outlier: 4.105A pdb=" N ASP E 117 " --> pdb=" O ARG E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 Processing helix chain 'E' and resid 248 through 271 removed outlier: 3.734A pdb=" N SER E 254 " --> pdb=" O TYR E 250 " (cutoff:3.500A) Proline residue: E 257 - end of helix removed outlier: 4.041A pdb=" N SER E 268 " --> pdb=" O MET E 264 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE E 269 " --> pdb=" O SER E 265 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TRP E 270 " --> pdb=" O TRP E 266 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE E 271 " --> pdb=" O VAL E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 300 Processing helix chain 'E' and resid 308 through 336 Processing helix chain 'E' and resid 425 through 451 Proline residue: E 436 - end of helix Processing helix chain 'K' and resid 495 through 497 No H-bonds generated for 'chain 'K' and resid 495 through 497' Processing helix chain 'L' and resid 495 through 497 No H-bonds generated for 'chain 'L' and resid 495 through 497' Processing helix chain 'M' and resid 495 through 497 No H-bonds generated for 'chain 'M' and resid 495 through 497' Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.476A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.681A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.868A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A 190 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 82 through 83 removed outlier: 4.476A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.682A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.868A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 82 through 83 removed outlier: 4.477A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.681A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.868A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 82 through 83 removed outlier: 4.476A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.682A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL D 106 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ARG D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.868A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 109 through 111 removed outlier: 3.737A pdb=" N ILE E 144 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA E 163 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA E 129 " --> pdb=" O ALA E 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 109 through 111 removed outlier: 3.737A pdb=" N ILE E 144 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLU E 84 " --> pdb=" O HIS E 77 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N HIS E 77 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR E 86 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE E 75 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR E 88 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG E 96 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASN E 65 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL E 64 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N TYR E 195 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL E 66 " --> pdb=" O TYR E 195 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 124 through 126 removed outlier: 3.978A pdb=" N SER E 218 " --> pdb=" O HIS E 242 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ARG E 244 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE E 216 " --> pdb=" O ARG E 244 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 2 through 7 Processing sheet with id=AB8, first strand: chain 'K' and resid 10 through 11 removed outlier: 7.201A pdb=" N GLY K 10 " --> pdb=" O THR K 509 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE K 420 " --> pdb=" O LYS K 486 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET K 421 " --> pdb=" O ALA K 437 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA K 437 " --> pdb=" O MET K 421 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP K 423 " --> pdb=" O VAL K 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 10 through 11 removed outlier: 7.201A pdb=" N GLY K 10 " --> pdb=" O THR K 509 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR K 501 " --> pdb=" O ALA K 485 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 2 through 7 Processing sheet with id=AC2, first strand: chain 'L' and resid 10 through 11 removed outlier: 7.201A pdb=" N GLY L 10 " --> pdb=" O THR L 509 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE L 420 " --> pdb=" O LYS L 486 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N MET L 421 " --> pdb=" O ALA L 437 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA L 437 " --> pdb=" O MET L 421 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP L 423 " --> pdb=" O VAL L 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 11 removed outlier: 7.201A pdb=" N GLY L 10 " --> pdb=" O THR L 509 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR L 501 " --> pdb=" O ALA L 485 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 2 through 7 Processing sheet with id=AC5, first strand: chain 'M' and resid 10 through 11 removed outlier: 7.202A pdb=" N GLY M 10 " --> pdb=" O THR M 509 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N MET M 421 " --> pdb=" O ALA M 437 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA M 437 " --> pdb=" O MET M 421 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP M 423 " --> pdb=" O VAL M 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 10 through 11 removed outlier: 7.202A pdb=" N GLY M 10 " --> pdb=" O THR M 509 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR M 501 " --> pdb=" O ALA M 485 " (cutoff:3.500A) 941 hydrogen bonds defined for protein. 2660 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: 2.65 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5100 1.34 - 1.46: 4382 1.46 - 1.58: 7662 1.58 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 17300 Sorted by residual: bond pdb=" C10 EPE C 501 " pdb=" S EPE C 501 " ideal model delta sigma weight residual 1.804 1.766 0.038 2.00e-02 2.50e+03 3.52e+00 bond pdb=" C10 EPE D 501 " pdb=" S EPE D 501 " ideal model delta sigma weight residual 1.804 1.767 0.037 2.00e-02 2.50e+03 3.46e+00 bond pdb=" O3S EPE C 501 " pdb=" S EPE C 501 " ideal model delta sigma weight residual 1.477 1.441 0.036 2.00e-02 2.50e+03 3.32e+00 bond pdb=" C10 EPE B 501 " pdb=" S EPE B 501 " ideal model delta sigma weight residual 1.804 1.768 0.036 2.00e-02 2.50e+03 3.21e+00 bond pdb=" O2S EPE C 501 " pdb=" S EPE C 501 " ideal model delta sigma weight residual 1.477 1.442 0.035 2.00e-02 2.50e+03 3.05e+00 ... (remaining 17295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 22935 1.12 - 2.24: 445 2.24 - 3.35: 170 3.35 - 4.47: 30 4.47 - 5.59: 15 Bond angle restraints: 23595 Sorted by residual: angle pdb=" C1 BMA F 3 " pdb=" O5 BMA F 3 " pdb=" C5 BMA F 3 " ideal model delta sigma weight residual 118.82 113.42 5.40 3.00e+00 1.11e-01 3.25e+00 angle pdb=" C1 BMA G 3 " pdb=" O5 BMA G 3 " pdb=" C5 BMA G 3 " ideal model delta sigma weight residual 118.82 113.57 5.25 3.00e+00 1.11e-01 3.06e+00 angle pdb=" C1 BMA H 3 " pdb=" O5 BMA H 3 " pdb=" C5 BMA H 3 " ideal model delta sigma weight residual 118.82 113.58 5.24 3.00e+00 1.11e-01 3.05e+00 angle pdb=" C1 BMA I 3 " pdb=" O5 BMA I 3 " pdb=" C5 BMA I 3 " ideal model delta sigma weight residual 118.82 113.70 5.12 3.00e+00 1.11e-01 2.92e+00 angle pdb=" CA TYR D 66 " pdb=" CB TYR D 66 " pdb=" CG TYR D 66 " ideal model delta sigma weight residual 113.90 116.88 -2.98 1.80e+00 3.09e-01 2.74e+00 ... (remaining 23590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.65: 10320 23.65 - 47.30: 110 47.30 - 70.94: 8 70.94 - 94.59: 29 94.59 - 118.24: 34 Dihedral angle restraints: 10501 sinusoidal: 4495 harmonic: 6006 Sorted by residual: dihedral pdb=" N1 EPE D 501 " pdb=" C5 EPE D 501 " pdb=" C6 EPE D 501 " pdb=" N4 EPE D 501 " ideal model delta sinusoidal sigma weight residual -58.50 59.74 -118.24 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C2 EPE C 501 " pdb=" C6 EPE C 501 " pdb=" N1 EPE C 501 " pdb=" C5 EPE C 501 " ideal model delta sinusoidal sigma weight residual 58.85 -59.32 118.17 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" N1 EPE B 501 " pdb=" C5 EPE B 501 " pdb=" C6 EPE B 501 " pdb=" N4 EPE B 501 " ideal model delta sinusoidal sigma weight residual -58.50 59.53 -118.03 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 10498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2281 0.053 - 0.106: 344 0.106 - 0.158: 58 0.158 - 0.211: 7 0.211 - 0.264: 5 Chirality restraints: 2695 Sorted by residual: chirality pdb=" C1 MAN F 5 " pdb=" O6 BMA F 3 " pdb=" C2 MAN F 5 " pdb=" O5 MAN F 5 " both_signs ideal model delta sigma weight residual False 2.40 2.31 0.09 2.00e-02 2.50e+03 2.23e+01 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.01e+01 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.75e+01 ... (remaining 2692 not shown) Planarity restraints: 2905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 501 " -0.028 2.00e-02 2.50e+03 2.33e-02 6.77e+00 pdb=" C7 NAG E 501 " 0.006 2.00e-02 2.50e+03 pdb=" C8 NAG E 501 " -0.021 2.00e-02 2.50e+03 pdb=" N2 NAG E 501 " 0.038 2.00e-02 2.50e+03 pdb=" O7 NAG E 501 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET E 256 " 0.039 5.00e-02 4.00e+02 5.91e-02 5.59e+00 pdb=" N PRO E 257 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO E 257 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 257 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 435 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO E 436 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO E 436 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 436 " 0.019 5.00e-02 4.00e+02 ... (remaining 2902 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1266 2.74 - 3.28: 16355 3.28 - 3.82: 28937 3.82 - 4.36: 36209 4.36 - 4.90: 61152 Nonbonded interactions: 143919 Sorted by model distance: nonbonded pdb=" ND2AASN A 41 " pdb=" O ARG A 169 " model vdw 2.205 3.120 nonbonded pdb=" OH TYR E 171 " pdb=" OH TYR E 250 " model vdw 2.209 3.040 nonbonded pdb=" OD2 ASP A 146 " pdb=" NE2 GLN A 148 " model vdw 2.324 3.120 nonbonded pdb=" OD2 ASP B 146 " pdb=" NE2 GLN B 148 " model vdw 2.324 3.120 nonbonded pdb=" OD2 ASP D 146 " pdb=" NE2 GLN D 148 " model vdw 2.325 3.120 ... (remaining 143914 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 40 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 65 or resid 67 through 103 or resid 105 through 111 or resi \ d 113 through 124 or resid 126 through 208 or resid 210 through 213 or resid 215 \ through 228 or resid 230 through 240 or resid 243 through 252 or resid 254 thro \ ugh 425 or resid 427 through 447)) selection = (chain 'B' and (resid 7 through 40 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 65 or resid 67 through 103 or resid 105 through 111 or resi \ d 113 through 124 or resid 126 through 208 or resid 210 through 213 or resid 215 \ through 228 or resid 230 through 240 or resid 243 through 252 or resid 254 thro \ ugh 425 or resid 427 through 447)) selection = (chain 'C' and (resid 7 through 40 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 65 or resid 67 through 103 or resid 105 through 111 or resi \ d 113 through 124 or resid 126 through 208 or resid 210 through 213 or resid 215 \ through 228 or resid 230 through 240 or resid 243 through 252 or resid 254 thro \ ugh 425 or resid 427 through 447)) selection = (chain 'D' and (resid 7 through 40 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 65 or resid 67 through 103 or resid 105 through 111 or resi \ d 113 through 124 or resid 126 through 208 or resid 210 through 213 or resid 215 \ through 228 or resid 230 through 240 or resid 243 through 252 or resid 254 thro \ ugh 425 or resid 427 through 447)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.98 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: 1.970 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: 0.040 Set scattering table: 0.050 Process input model: 17.690 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.300 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: 0.8325 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17337 Z= 0.128 Angle : 0.470 9.122 23698 Z= 0.214 Chirality : 0.042 0.264 2695 Planarity : 0.003 0.059 2896 Dihedral : 12.100 118.241 6661 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.39 % Allowed : 2.47 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % 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: 2.50 (0.20), residues: 2027 helix: 2.53 (0.21), residues: 583 sheet: 1.62 (0.22), residues: 644 loop : 1.17 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 196 TYR 0.015 0.001 TYR D 66 PHE 0.006 0.001 PHE E 115 TRP 0.007 0.001 TRP A 426 HIS 0.001 0.000 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00259 (17300) covalent geometry : angle 0.45872 (23595) SS BOND : bond 0.00051 ( 8) SS BOND : angle 0.41957 ( 16) hydrogen bonds : bond 0.21331 ( 838) hydrogen bonds : angle 7.12400 ( 2660) link_ALPHA1-3 : bond 0.00166 ( 4) link_ALPHA1-3 : angle 1.03980 ( 12) link_ALPHA1-6 : bond 0.00067 ( 4) link_ALPHA1-6 : angle 1.15856 ( 12) link_BETA1-4 : bond 0.00128 ( 12) link_BETA1-4 : angle 1.13529 ( 36) link_NAG-ASN : bond 0.00109 ( 9) link_NAG-ASN : angle 2.64901 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 543 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 TYR cc_start: 0.7908 (p90) cc_final: 0.7419 (p90) REVERT: A 277 TYR cc_start: 0.8246 (p90) cc_final: 0.8010 (p90) REVERT: A 306 PHE cc_start: 0.7443 (t80) cc_final: 0.6816 (t80) REVERT: A 433 PHE cc_start: 0.7807 (t80) cc_final: 0.7474 (t80) REVERT: B 304 TYR cc_start: 0.8608 (t80) cc_final: 0.8388 (t80) REVERT: C 141 ARG cc_start: 0.7900 (mtt90) cc_final: 0.7651 (mtt-85) REVERT: C 274 LYS cc_start: 0.8012 (mttt) cc_final: 0.7778 (mptt) REVERT: C 434 THR cc_start: 0.9243 (m) cc_final: 0.8932 (p) REVERT: D 227 MET cc_start: 0.7140 (mmt) cc_final: 0.6633 (mmm) REVERT: D 243 ASN cc_start: 0.8072 (t0) cc_final: 0.7854 (t0) REVERT: D 271 THR cc_start: 0.8687 (p) cc_final: 0.8476 (p) REVERT: E 244 ARG cc_start: 0.7753 (ttt-90) cc_final: 0.7531 (ttt-90) REVERT: E 310 LEU cc_start: 0.8476 (tp) cc_final: 0.8249 (tp) REVERT: E 330 PHE cc_start: 0.7626 (t80) cc_final: 0.7324 (t80) REVERT: K 468 LEU cc_start: 0.7719 (tp) cc_final: 0.7017 (tp) REVERT: K 495 TYR cc_start: 0.8360 (m-80) cc_final: 0.8007 (m-80) REVERT: L 407 LEU cc_start: 0.8228 (mt) cc_final: 0.7938 (mm) REVERT: L 472 ASN cc_start: 0.8035 (t0) cc_final: 0.7714 (t0) outliers start: 6 outliers final: 1 residues processed: 548 average time/residue: 0.5600 time to fit residues: 341.2701 Evaluate side-chains 350 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 349 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 103 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.0030 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN D 439 ASN E 147 GLN E 200 GLN E 213 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.118513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.081159 restraints weight = 180977.225| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 5.50 r_work: 0.2815 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17337 Z= 0.145 Angle : 0.641 8.514 23698 Z= 0.327 Chirality : 0.046 0.224 2695 Planarity : 0.004 0.069 2896 Dihedral : 12.207 111.132 2931 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.82 % Allowed : 15.71 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % 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: 2.34 (0.19), residues: 2027 helix: 2.32 (0.21), residues: 595 sheet: 1.59 (0.22), residues: 587 loop : 1.12 (0.23), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 68 TYR 0.023 0.002 TYR B 244 PHE 0.024 0.002 PHE D 301 TRP 0.014 0.001 TRP B 237 HIS 0.004 0.001 HIS E 240 Details of bonding type rmsd covalent geometry : bond 0.00315 (17300) covalent geometry : angle 0.62972 (23595) SS BOND : bond 0.00236 ( 8) SS BOND : angle 0.49602 ( 16) hydrogen bonds : bond 0.04575 ( 838) hydrogen bonds : angle 4.88922 ( 2660) link_ALPHA1-3 : bond 0.00820 ( 4) link_ALPHA1-3 : angle 2.43855 ( 12) link_ALPHA1-6 : bond 0.00508 ( 4) link_ALPHA1-6 : angle 1.85821 ( 12) link_BETA1-4 : bond 0.00274 ( 12) link_BETA1-4 : angle 1.68363 ( 36) link_NAG-ASN : bond 0.00193 ( 9) link_NAG-ASN : angle 2.53808 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 392 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.7262 (pmm) cc_final: 0.6962 (mtm) REVERT: A 90 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8647 (pm20) REVERT: A 244 TYR cc_start: 0.8126 (p90) cc_final: 0.7549 (p90) REVERT: A 277 TYR cc_start: 0.8240 (p90) cc_final: 0.7948 (p90) REVERT: A 306 PHE cc_start: 0.8093 (t80) cc_final: 0.7440 (t80) REVERT: B 265 ASN cc_start: 0.8315 (t0) cc_final: 0.8017 (t0) REVERT: B 279 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8339 (mttt) REVERT: B 304 TYR cc_start: 0.8682 (t80) cc_final: 0.8396 (t80) REVERT: C 21 LYS cc_start: 0.8485 (mmmm) cc_final: 0.8105 (mptt) REVERT: C 141 ARG cc_start: 0.8664 (mtt90) cc_final: 0.8261 (mtm180) REVERT: C 235 LEU cc_start: 0.8705 (tp) cc_final: 0.8423 (tt) REVERT: C 244 TYR cc_start: 0.7752 (p90) cc_final: 0.7525 (p90) REVERT: C 274 LYS cc_start: 0.8102 (mttt) cc_final: 0.7666 (mptt) REVERT: C 302 VAL cc_start: 0.8496 (p) cc_final: 0.8280 (m) REVERT: C 434 THR cc_start: 0.9185 (m) cc_final: 0.8945 (p) REVERT: D 9 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.7057 (ptt) REVERT: D 182 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7422 (mp0) REVERT: D 227 MET cc_start: 0.7339 (mmt) cc_final: 0.7074 (mmm) REVERT: D 230 ILE cc_start: 0.8689 (pp) cc_final: 0.8487 (pp) REVERT: D 243 ASN cc_start: 0.8402 (t0) cc_final: 0.7990 (t0) REVERT: D 274 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8047 (mmmm) REVERT: D 294 LEU cc_start: 0.8811 (mt) cc_final: 0.8406 (mp) REVERT: E 83 MET cc_start: 0.9208 (mmt) cc_final: 0.8958 (mmt) REVERT: E 107 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6666 (pm20) REVERT: E 208 LYS cc_start: 0.8971 (mttm) cc_final: 0.8560 (mtpt) REVERT: E 250 TYR cc_start: 0.7207 (t80) cc_final: 0.6950 (t80) REVERT: E 260 LEU cc_start: 0.8630 (pp) cc_final: 0.8346 (mm) REVERT: E 330 PHE cc_start: 0.7668 (t80) cc_final: 0.7337 (t80) REVERT: K 407 LEU cc_start: 0.8392 (mt) cc_final: 0.7950 (mp) REVERT: K 408 SER cc_start: 0.7546 (OUTLIER) cc_final: 0.7290 (t) REVERT: K 470 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7424 (mpt) REVERT: K 495 TYR cc_start: 0.8692 (m-80) cc_final: 0.8374 (m-80) REVERT: L 1 GLN cc_start: 0.7958 (mp10) cc_final: 0.7504 (mp10) REVERT: L 3 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8471 (mp10) REVERT: L 460 ASP cc_start: 0.5785 (OUTLIER) cc_final: 0.5534 (p0) REVERT: L 469 GLU cc_start: 0.7836 (mp0) cc_final: 0.7487 (mp0) REVERT: L 472 ASN cc_start: 0.8151 (t0) cc_final: 0.7913 (t0) REVERT: M 412 SER cc_start: 0.8472 (p) cc_final: 0.8009 (p) outliers start: 65 outliers final: 24 residues processed: 418 average time/residue: 0.5472 time to fit residues: 258.3743 Evaluate side-chains 377 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 345 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 279 LYS Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 430 TYR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 458 SER Chi-restraints excluded: chain K residue 470 MET Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 460 ASP Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 450 SER Chi-restraints excluded: chain M residue 452 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 84 optimal weight: 0.8980 chunk 182 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 79 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN A 224 GLN C 185 GLN E 147 GLN M 464 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.112824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.074694 restraints weight = 164515.216| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 5.52 r_work: 0.2676 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 17337 Z= 0.211 Angle : 0.678 12.228 23698 Z= 0.339 Chirality : 0.047 0.216 2695 Planarity : 0.004 0.070 2896 Dihedral : 11.957 116.365 2929 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 4.15 % Allowed : 16.39 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % 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: 1.93 (0.19), residues: 2027 helix: 1.92 (0.20), residues: 595 sheet: 1.33 (0.21), residues: 629 loop : 0.91 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 142 TYR 0.028 0.002 TYR D 299 PHE 0.025 0.002 PHE A 433 TRP 0.010 0.001 TRP L 440 HIS 0.005 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00475 (17300) covalent geometry : angle 0.66559 (23595) SS BOND : bond 0.00251 ( 8) SS BOND : angle 0.74944 ( 16) hydrogen bonds : bond 0.04666 ( 838) hydrogen bonds : angle 4.84634 ( 2660) link_ALPHA1-3 : bond 0.00986 ( 4) link_ALPHA1-3 : angle 1.70659 ( 12) link_ALPHA1-6 : bond 0.00775 ( 4) link_ALPHA1-6 : angle 1.76644 ( 12) link_BETA1-4 : bond 0.00312 ( 12) link_BETA1-4 : angle 1.86924 ( 36) link_NAG-ASN : bond 0.00886 ( 9) link_NAG-ASN : angle 2.84144 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 352 time to evaluate : 0.599 Fit side-chains REVERT: A 90 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8731 (pm20) REVERT: A 165 GLU cc_start: 0.8733 (tt0) cc_final: 0.8506 (tp30) REVERT: A 244 TYR cc_start: 0.8208 (p90) cc_final: 0.7698 (p90) REVERT: A 306 PHE cc_start: 0.8034 (t80) cc_final: 0.7662 (t80) REVERT: B 265 ASN cc_start: 0.8395 (t0) cc_final: 0.8188 (t0) REVERT: C 61 MET cc_start: 0.9475 (OUTLIER) cc_final: 0.9236 (ptt) REVERT: C 141 ARG cc_start: 0.8749 (mtt90) cc_final: 0.8397 (mtm180) REVERT: C 235 LEU cc_start: 0.8688 (tp) cc_final: 0.8472 (tt) REVERT: C 244 TYR cc_start: 0.8112 (p90) cc_final: 0.7841 (p90) REVERT: C 274 LYS cc_start: 0.8124 (mttt) cc_final: 0.7917 (mmmm) REVERT: C 434 THR cc_start: 0.9089 (m) cc_final: 0.8851 (p) REVERT: D 68 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8927 (tpp80) REVERT: D 227 MET cc_start: 0.7434 (mmt) cc_final: 0.7136 (mmm) REVERT: D 230 ILE cc_start: 0.8642 (pp) cc_final: 0.8412 (pp) REVERT: D 243 ASN cc_start: 0.8460 (t0) cc_final: 0.7924 (t0) REVERT: D 274 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8136 (mmmm) REVERT: E 208 LYS cc_start: 0.8945 (mttm) cc_final: 0.8582 (mtpt) REVERT: E 250 TYR cc_start: 0.7515 (t80) cc_final: 0.7074 (t80) REVERT: E 253 GLN cc_start: 0.7553 (tt0) cc_final: 0.7351 (pt0) REVERT: E 330 PHE cc_start: 0.7808 (t80) cc_final: 0.7478 (t80) REVERT: K 407 LEU cc_start: 0.8484 (mt) cc_final: 0.8068 (mp) REVERT: K 426 GLN cc_start: 0.7364 (pm20) cc_final: 0.7161 (pm20) REVERT: K 470 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7585 (mpt) REVERT: L 469 GLU cc_start: 0.8055 (mp0) cc_final: 0.7723 (mp0) REVERT: L 472 ASN cc_start: 0.8262 (t0) cc_final: 0.7837 (t0) REVERT: L 474 LYS cc_start: 0.7901 (mtmt) cc_final: 0.7583 (mtmm) outliers start: 70 outliers final: 32 residues processed: 384 average time/residue: 0.5542 time to fit residues: 238.4353 Evaluate side-chains 350 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 313 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 470 MET Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 490 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 141 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 98 optimal weight: 0.4980 chunk 165 optimal weight: 10.0000 chunk 161 optimal weight: 20.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN C 243 ASN C 265 ASN E 147 GLN E 213 GLN K 471 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.114034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.076057 restraints weight = 165604.178| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 5.22 r_work: 0.2717 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17337 Z= 0.133 Angle : 0.634 15.295 23698 Z= 0.311 Chirality : 0.047 0.621 2695 Planarity : 0.004 0.068 2896 Dihedral : 11.365 117.102 2929 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.76 % Allowed : 17.73 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % 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: 1.80 (0.19), residues: 2027 helix: 1.84 (0.20), residues: 602 sheet: 1.47 (0.22), residues: 564 loop : 0.66 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 142 TYR 0.024 0.001 TYR C 299 PHE 0.027 0.002 PHE A 433 TRP 0.011 0.001 TRP B 237 HIS 0.002 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00289 (17300) covalent geometry : angle 0.61657 (23595) SS BOND : bond 0.00176 ( 8) SS BOND : angle 0.38212 ( 16) hydrogen bonds : bond 0.03870 ( 838) hydrogen bonds : angle 4.56505 ( 2660) link_ALPHA1-3 : bond 0.01039 ( 4) link_ALPHA1-3 : angle 2.03902 ( 12) link_ALPHA1-6 : bond 0.00912 ( 4) link_ALPHA1-6 : angle 1.78531 ( 12) link_BETA1-4 : bond 0.00245 ( 12) link_BETA1-4 : angle 1.57771 ( 36) link_NAG-ASN : bond 0.00362 ( 9) link_NAG-ASN : angle 3.67093 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 332 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.7499 (pmm) cc_final: 0.6887 (tpp) REVERT: A 13 LYS cc_start: 0.8549 (mtpp) cc_final: 0.7760 (mttp) REVERT: A 90 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8670 (pm20) REVERT: A 141 ARG cc_start: 0.8311 (mtm-85) cc_final: 0.7899 (mpt180) REVERT: A 244 TYR cc_start: 0.8217 (p90) cc_final: 0.7692 (p90) REVERT: A 277 TYR cc_start: 0.8127 (p90) cc_final: 0.7864 (p90) REVERT: A 306 PHE cc_start: 0.8018 (t80) cc_final: 0.7587 (t80) REVERT: C 21 LYS cc_start: 0.8576 (mmmm) cc_final: 0.8211 (mptt) REVERT: C 141 ARG cc_start: 0.8764 (mtt90) cc_final: 0.8432 (mtm180) REVERT: C 235 LEU cc_start: 0.8698 (tp) cc_final: 0.8485 (tt) REVERT: C 244 TYR cc_start: 0.8140 (p90) cc_final: 0.7863 (p90) REVERT: C 274 LYS cc_start: 0.8086 (mttt) cc_final: 0.7875 (mmmm) REVERT: C 305 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8107 (mp) REVERT: C 434 THR cc_start: 0.9095 (m) cc_final: 0.8839 (p) REVERT: D 9 MET cc_start: 0.7295 (ttp) cc_final: 0.7012 (ptt) REVERT: D 215 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8726 (ttpp) REVERT: D 227 MET cc_start: 0.7411 (mmt) cc_final: 0.7185 (mmm) REVERT: D 243 ASN cc_start: 0.8443 (t0) cc_final: 0.7840 (t0) REVERT: D 274 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8125 (mmmm) REVERT: E 118 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8822 (mtmm) REVERT: E 208 LYS cc_start: 0.8925 (mttm) cc_final: 0.8572 (mtpt) REVERT: E 250 TYR cc_start: 0.7472 (t80) cc_final: 0.7042 (t80) REVERT: E 253 GLN cc_start: 0.7564 (tt0) cc_final: 0.7358 (pt0) REVERT: E 330 PHE cc_start: 0.7794 (t80) cc_final: 0.7421 (t80) REVERT: K 407 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8113 (mp) REVERT: K 426 GLN cc_start: 0.6896 (pm20) cc_final: 0.6633 (pm20) REVERT: K 470 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7584 (mpt) REVERT: L 1 GLN cc_start: 0.8034 (mp10) cc_final: 0.7828 (mp10) REVERT: L 469 GLU cc_start: 0.8080 (mp0) cc_final: 0.7701 (mp0) REVERT: M 472 ASN cc_start: 0.8366 (t0) cc_final: 0.8158 (t0) outliers start: 63 outliers final: 27 residues processed: 361 average time/residue: 0.5216 time to fit residues: 212.2476 Evaluate side-chains 343 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 309 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 407 LEU Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 470 MET Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 490 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 69 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 185 optimal weight: 20.0000 chunk 27 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN E 147 GLN E 213 GLN K 471 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.113240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.075107 restraints weight = 150822.496| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 5.05 r_work: 0.2702 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17337 Z= 0.156 Angle : 0.634 12.800 23698 Z= 0.312 Chirality : 0.047 0.557 2695 Planarity : 0.004 0.066 2896 Dihedral : 10.751 114.260 2929 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.98 % Allowed : 18.29 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % 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: 1.75 (0.19), residues: 2027 helix: 1.82 (0.21), residues: 602 sheet: 1.47 (0.22), residues: 560 loop : 0.59 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 269 TYR 0.022 0.002 TYR E 318 PHE 0.029 0.002 PHE A 433 TRP 0.016 0.001 TRP L 440 HIS 0.003 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00347 (17300) covalent geometry : angle 0.61912 (23595) SS BOND : bond 0.00187 ( 8) SS BOND : angle 0.50680 ( 16) hydrogen bonds : bond 0.03820 ( 838) hydrogen bonds : angle 4.50655 ( 2660) link_ALPHA1-3 : bond 0.01018 ( 4) link_ALPHA1-3 : angle 2.05871 ( 12) link_ALPHA1-6 : bond 0.00910 ( 4) link_ALPHA1-6 : angle 1.76210 ( 12) link_BETA1-4 : bond 0.00265 ( 12) link_BETA1-4 : angle 1.67059 ( 36) link_NAG-ASN : bond 0.00635 ( 9) link_NAG-ASN : angle 3.30049 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 342 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8594 (mtpp) cc_final: 0.7948 (mttp) REVERT: A 90 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8696 (pm20) REVERT: A 141 ARG cc_start: 0.8325 (mtm-85) cc_final: 0.7977 (mpt180) REVERT: A 244 TYR cc_start: 0.8202 (p90) cc_final: 0.7704 (p90) REVERT: A 306 PHE cc_start: 0.8003 (t80) cc_final: 0.7511 (t80) REVERT: A 426 TRP cc_start: 0.7962 (m-90) cc_final: 0.7464 (m-10) REVERT: B 14 GLU cc_start: 0.8851 (pt0) cc_final: 0.8647 (pt0) REVERT: B 298 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8402 (pp20) REVERT: C 21 LYS cc_start: 0.8689 (mmmm) cc_final: 0.8347 (mptt) REVERT: C 61 MET cc_start: 0.9435 (ptt) cc_final: 0.9215 (ptt) REVERT: C 141 ARG cc_start: 0.8724 (mtt90) cc_final: 0.8440 (mtm180) REVERT: C 235 LEU cc_start: 0.8723 (tp) cc_final: 0.8514 (tt) REVERT: C 244 TYR cc_start: 0.8254 (p90) cc_final: 0.7955 (p90) REVERT: C 274 LYS cc_start: 0.8064 (mttt) cc_final: 0.7774 (mmmm) REVERT: C 305 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8041 (mp) REVERT: C 434 THR cc_start: 0.9126 (m) cc_final: 0.8883 (p) REVERT: D 18 LYS cc_start: 0.8726 (mmtm) cc_final: 0.8526 (mmtm) REVERT: D 215 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8746 (ttpp) REVERT: D 243 ASN cc_start: 0.8483 (t0) cc_final: 0.7830 (t0) REVERT: D 274 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8178 (mmmm) REVERT: D 425 ARG cc_start: 0.8134 (ppt170) cc_final: 0.7898 (ppt170) REVERT: E 118 LYS cc_start: 0.9142 (mtmm) cc_final: 0.8854 (mtmm) REVERT: E 208 LYS cc_start: 0.8896 (mttm) cc_final: 0.8554 (mtpt) REVERT: E 330 PHE cc_start: 0.7828 (t80) cc_final: 0.7521 (t80) REVERT: K 407 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8127 (mp) REVERT: K 470 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7299 (mpt) REVERT: K 482 TYR cc_start: 0.8965 (m-80) cc_final: 0.8343 (m-80) REVERT: K 504 GLN cc_start: 0.8343 (mp10) cc_final: 0.8089 (mp10) REVERT: L 469 GLU cc_start: 0.8109 (mp0) cc_final: 0.7684 (mp0) REVERT: M 426 GLN cc_start: 0.8225 (tt0) cc_final: 0.7380 (tp40) REVERT: M 438 ILE cc_start: 0.9058 (tt) cc_final: 0.8851 (tp) outliers start: 66 outliers final: 34 residues processed: 370 average time/residue: 0.5353 time to fit residues: 222.6673 Evaluate side-chains 354 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 314 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 430 TYR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 407 LEU Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 470 MET Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 490 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 168 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 chunk 185 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 82 optimal weight: 0.0970 chunk 75 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 133 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN C 64 GLN C 185 GLN E 147 GLN E 213 GLN E 253 GLN K 471 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.113975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.076151 restraints weight = 170513.519| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 5.25 r_work: 0.2721 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17337 Z= 0.121 Angle : 0.623 12.109 23698 Z= 0.306 Chirality : 0.046 0.491 2695 Planarity : 0.003 0.067 2896 Dihedral : 10.358 112.015 2929 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.03 % Allowed : 19.92 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % 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: 1.71 (0.19), residues: 2027 helix: 1.78 (0.21), residues: 602 sheet: 1.41 (0.22), residues: 563 loop : 0.60 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 142 TYR 0.022 0.001 TYR E 318 PHE 0.028 0.001 PHE A 433 TRP 0.023 0.001 TRP B 237 HIS 0.003 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00265 (17300) covalent geometry : angle 0.61044 (23595) SS BOND : bond 0.00166 ( 8) SS BOND : angle 0.29596 ( 16) hydrogen bonds : bond 0.03643 ( 838) hydrogen bonds : angle 4.42528 ( 2660) link_ALPHA1-3 : bond 0.01069 ( 4) link_ALPHA1-3 : angle 1.99256 ( 12) link_ALPHA1-6 : bond 0.00982 ( 4) link_ALPHA1-6 : angle 1.70913 ( 12) link_BETA1-4 : bond 0.00303 ( 12) link_BETA1-4 : angle 1.48861 ( 36) link_NAG-ASN : bond 0.00539 ( 9) link_NAG-ASN : angle 3.03145 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 329 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6758 (mmm) cc_final: 0.6350 (tpt) REVERT: A 13 LYS cc_start: 0.8585 (mtpp) cc_final: 0.7895 (mttp) REVERT: A 90 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8666 (pm20) REVERT: A 141 ARG cc_start: 0.8308 (mtm-85) cc_final: 0.7975 (mpt180) REVERT: A 244 TYR cc_start: 0.8185 (p90) cc_final: 0.7666 (p90) REVERT: A 277 TYR cc_start: 0.8092 (p90) cc_final: 0.7838 (p90) REVERT: A 306 PHE cc_start: 0.7917 (t80) cc_final: 0.7505 (t80) REVERT: A 426 TRP cc_start: 0.7958 (m-90) cc_final: 0.7476 (m-10) REVERT: B 305 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8713 (mp) REVERT: C 21 LYS cc_start: 0.8667 (mmmm) cc_final: 0.8340 (mptt) REVERT: C 61 MET cc_start: 0.9447 (ptt) cc_final: 0.9195 (ptt) REVERT: C 141 ARG cc_start: 0.8729 (mtt90) cc_final: 0.8443 (mtm180) REVERT: C 235 LEU cc_start: 0.8722 (tp) cc_final: 0.8497 (tt) REVERT: C 244 TYR cc_start: 0.8312 (p90) cc_final: 0.8006 (p90) REVERT: C 274 LYS cc_start: 0.8103 (mttt) cc_final: 0.7595 (mmmm) REVERT: C 305 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8041 (mp) REVERT: C 434 THR cc_start: 0.9114 (m) cc_final: 0.8870 (p) REVERT: D 9 MET cc_start: 0.7247 (ptp) cc_final: 0.6977 (ptt) REVERT: D 18 LYS cc_start: 0.8744 (mmtm) cc_final: 0.8530 (mmtm) REVERT: D 215 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8708 (ttpp) REVERT: D 243 ASN cc_start: 0.8533 (t0) cc_final: 0.7896 (t0) REVERT: D 274 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8096 (mmmm) REVERT: D 286 MET cc_start: 0.8638 (mtm) cc_final: 0.8423 (mtm) REVERT: D 425 ARG cc_start: 0.8162 (ppt170) cc_final: 0.7922 (ppt170) REVERT: E 118 LYS cc_start: 0.9104 (mtmm) cc_final: 0.8793 (mtmm) REVERT: E 208 LYS cc_start: 0.8907 (mttm) cc_final: 0.8559 (mtpt) REVERT: E 250 TYR cc_start: 0.7432 (t80) cc_final: 0.7041 (t80) REVERT: E 290 MET cc_start: 0.8984 (tpp) cc_final: 0.8703 (tpt) REVERT: E 330 PHE cc_start: 0.7787 (t80) cc_final: 0.7473 (t80) REVERT: K 407 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8106 (mp) REVERT: K 426 GLN cc_start: 0.6946 (pt0) cc_final: 0.6545 (pt0) REVERT: K 469 GLU cc_start: 0.8108 (mp0) cc_final: 0.7848 (mp0) REVERT: K 470 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7321 (mpt) REVERT: K 482 TYR cc_start: 0.9003 (m-80) cc_final: 0.8265 (m-80) REVERT: L 469 GLU cc_start: 0.8087 (mp0) cc_final: 0.7743 (mp0) REVERT: M 426 GLN cc_start: 0.8219 (tt0) cc_final: 0.7412 (tp40) outliers start: 49 outliers final: 25 residues processed: 348 average time/residue: 0.5507 time to fit residues: 214.9642 Evaluate side-chains 349 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 317 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 407 LEU Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 470 MET Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 490 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 99 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN E 147 GLN E 213 GLN K 471 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.110733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.072341 restraints weight = 167114.015| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 5.52 r_work: 0.2631 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17337 Z= 0.249 Angle : 0.706 12.718 23698 Z= 0.351 Chirality : 0.049 0.461 2695 Planarity : 0.004 0.066 2896 Dihedral : 10.472 118.013 2929 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.20 % Allowed : 19.87 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % 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: 1.52 (0.19), residues: 2027 helix: 1.67 (0.21), residues: 602 sheet: 1.13 (0.21), residues: 588 loop : 0.57 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 454 TYR 0.023 0.002 TYR C 299 PHE 0.029 0.002 PHE A 433 TRP 0.025 0.002 TRP L 440 HIS 0.004 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00568 (17300) covalent geometry : angle 0.69183 (23595) SS BOND : bond 0.00171 ( 8) SS BOND : angle 0.87386 ( 16) hydrogen bonds : bond 0.04081 ( 838) hydrogen bonds : angle 4.68136 ( 2660) link_ALPHA1-3 : bond 0.00747 ( 4) link_ALPHA1-3 : angle 2.34349 ( 12) link_ALPHA1-6 : bond 0.00722 ( 4) link_ALPHA1-6 : angle 1.74026 ( 12) link_BETA1-4 : bond 0.00419 ( 12) link_BETA1-4 : angle 1.94229 ( 36) link_NAG-ASN : bond 0.00611 ( 9) link_NAG-ASN : angle 3.20172 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 343 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.6957 (mmm) cc_final: 0.6631 (tpt) REVERT: A 13 LYS cc_start: 0.8637 (mtpp) cc_final: 0.7996 (mttp) REVERT: A 90 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8823 (pm20) REVERT: A 141 ARG cc_start: 0.8376 (mtm-85) cc_final: 0.8004 (mpt180) REVERT: A 244 TYR cc_start: 0.8210 (p90) cc_final: 0.7819 (p90) REVERT: A 306 PHE cc_start: 0.7946 (t80) cc_final: 0.7701 (t80) REVERT: A 426 TRP cc_start: 0.8037 (m-90) cc_final: 0.7494 (m-10) REVERT: C 21 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8438 (mptt) REVERT: C 61 MET cc_start: 0.9504 (ptt) cc_final: 0.9285 (ptt) REVERT: C 141 ARG cc_start: 0.8774 (mtt90) cc_final: 0.8462 (mtm180) REVERT: C 235 LEU cc_start: 0.8732 (tp) cc_final: 0.8509 (tt) REVERT: C 244 TYR cc_start: 0.8318 (p90) cc_final: 0.8049 (p90) REVERT: C 274 LYS cc_start: 0.8137 (mttt) cc_final: 0.7817 (mmmm) REVERT: C 305 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8008 (mp) REVERT: C 434 THR cc_start: 0.9082 (m) cc_final: 0.8839 (p) REVERT: D 215 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8782 (ttpp) REVERT: D 218 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6595 (mm) REVERT: D 243 ASN cc_start: 0.8493 (t0) cc_final: 0.7935 (t0) REVERT: D 274 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8240 (mmmm) REVERT: D 306 PHE cc_start: 0.8143 (t80) cc_final: 0.7710 (t80) REVERT: D 425 ARG cc_start: 0.8107 (ppt170) cc_final: 0.7866 (ppt170) REVERT: E 118 LYS cc_start: 0.9147 (mtmm) cc_final: 0.8905 (mtmm) REVERT: E 173 MET cc_start: 0.8906 (ptp) cc_final: 0.8669 (ptm) REVERT: E 208 LYS cc_start: 0.8932 (mttm) cc_final: 0.8580 (mtpt) REVERT: E 330 PHE cc_start: 0.7838 (t80) cc_final: 0.7550 (t80) REVERT: K 407 LEU cc_start: 0.8521 (mt) cc_final: 0.8263 (mp) REVERT: K 426 GLN cc_start: 0.7273 (pt0) cc_final: 0.6767 (pt0) REVERT: K 469 GLU cc_start: 0.8299 (mp0) cc_final: 0.8023 (mp0) REVERT: K 470 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7219 (mpt) REVERT: K 482 TYR cc_start: 0.9099 (m-80) cc_final: 0.8380 (m-80) REVERT: K 504 GLN cc_start: 0.8327 (mp10) cc_final: 0.7823 (pm20) REVERT: L 469 GLU cc_start: 0.8148 (mp0) cc_final: 0.7722 (mp0) REVERT: M 408 SER cc_start: 0.8257 (OUTLIER) cc_final: 0.7320 (p) REVERT: M 426 GLN cc_start: 0.8384 (tt0) cc_final: 0.7482 (tp40) REVERT: M 474 LYS cc_start: 0.8424 (ptpt) cc_final: 0.8069 (tmtm) outliers start: 52 outliers final: 32 residues processed: 367 average time/residue: 0.5492 time to fit residues: 226.1788 Evaluate side-chains 357 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 318 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 430 TYR Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 445 THR Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 470 MET Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 490 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 173 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 180 optimal weight: 0.0020 chunk 78 optimal weight: 1.9990 chunk 190 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN C 64 GLN E 147 GLN E 213 GLN K 471 ASN L 414 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.111069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.073024 restraints weight = 161000.089| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 5.06 r_work: 0.2663 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 17337 Z= 0.195 Angle : 0.670 12.943 23698 Z= 0.331 Chirality : 0.047 0.425 2695 Planarity : 0.004 0.063 2896 Dihedral : 10.326 114.720 2929 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.14 % Allowed : 20.31 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % 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: 1.48 (0.19), residues: 2027 helix: 1.59 (0.21), residues: 602 sheet: 1.15 (0.21), residues: 585 loop : 0.55 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 269 TYR 0.023 0.002 TYR A 299 PHE 0.028 0.002 PHE A 433 TRP 0.025 0.001 TRP L 440 HIS 0.004 0.001 HIS E 240 Details of bonding type rmsd covalent geometry : bond 0.00446 (17300) covalent geometry : angle 0.65748 (23595) SS BOND : bond 0.00167 ( 8) SS BOND : angle 0.61107 ( 16) hydrogen bonds : bond 0.03919 ( 838) hydrogen bonds : angle 4.59261 ( 2660) link_ALPHA1-3 : bond 0.00919 ( 4) link_ALPHA1-3 : angle 2.10048 ( 12) link_ALPHA1-6 : bond 0.00822 ( 4) link_ALPHA1-6 : angle 1.70834 ( 12) link_BETA1-4 : bond 0.00309 ( 12) link_BETA1-4 : angle 1.73734 ( 36) link_NAG-ASN : bond 0.00516 ( 9) link_NAG-ASN : angle 2.89008 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 350 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6890 (mmm) cc_final: 0.6539 (tpt) REVERT: A 13 LYS cc_start: 0.8667 (mtpp) cc_final: 0.8037 (mttp) REVERT: A 137 MET cc_start: 0.8578 (tpp) cc_final: 0.8261 (ptt) REVERT: A 141 ARG cc_start: 0.8367 (mtm-85) cc_final: 0.8012 (mpt180) REVERT: A 244 TYR cc_start: 0.8252 (p90) cc_final: 0.7877 (p90) REVERT: A 426 TRP cc_start: 0.8049 (m-90) cc_final: 0.7494 (m-10) REVERT: C 21 LYS cc_start: 0.8763 (mmmm) cc_final: 0.8444 (mptt) REVERT: C 61 MET cc_start: 0.9441 (ptt) cc_final: 0.9230 (ptt) REVERT: C 141 ARG cc_start: 0.8751 (mtt90) cc_final: 0.8463 (mtm180) REVERT: C 235 LEU cc_start: 0.8771 (tp) cc_final: 0.8551 (tt) REVERT: C 244 TYR cc_start: 0.8372 (p90) cc_final: 0.8118 (p90) REVERT: C 274 LYS cc_start: 0.8156 (mttt) cc_final: 0.7857 (mmmm) REVERT: C 305 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8065 (mp) REVERT: C 434 THR cc_start: 0.9124 (m) cc_final: 0.8870 (p) REVERT: D 215 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8770 (ttpp) REVERT: D 218 ILE cc_start: 0.7191 (OUTLIER) cc_final: 0.6663 (mm) REVERT: D 243 ASN cc_start: 0.8495 (t0) cc_final: 0.7859 (t0) REVERT: D 274 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8189 (mmmm) REVERT: D 306 PHE cc_start: 0.8286 (t80) cc_final: 0.7734 (t80) REVERT: D 425 ARG cc_start: 0.8199 (ppt170) cc_final: 0.7948 (ppt170) REVERT: E 118 LYS cc_start: 0.9125 (mtmm) cc_final: 0.8873 (mtmm) REVERT: E 208 LYS cc_start: 0.8929 (mttm) cc_final: 0.8588 (mtpt) REVERT: E 330 PHE cc_start: 0.7897 (t80) cc_final: 0.7595 (t80) REVERT: K 407 LEU cc_start: 0.8416 (mt) cc_final: 0.8166 (mp) REVERT: K 426 GLN cc_start: 0.7307 (pt0) cc_final: 0.6832 (pt0) REVERT: K 447 TYR cc_start: 0.9091 (m-80) cc_final: 0.8791 (m-80) REVERT: K 469 GLU cc_start: 0.8141 (mp0) cc_final: 0.7896 (mp0) REVERT: K 470 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7116 (mpt) REVERT: K 482 TYR cc_start: 0.9046 (m-80) cc_final: 0.8354 (m-80) REVERT: K 504 GLN cc_start: 0.8384 (mp10) cc_final: 0.7806 (pm20) REVERT: L 1 GLN cc_start: 0.7943 (mp10) cc_final: 0.7701 (pm20) REVERT: L 469 GLU cc_start: 0.8215 (mp0) cc_final: 0.7764 (mp0) REVERT: M 408 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.7416 (p) REVERT: M 426 GLN cc_start: 0.8385 (tt0) cc_final: 0.7582 (tp40) REVERT: M 466 VAL cc_start: 0.8198 (t) cc_final: 0.7817 (p) REVERT: M 474 LYS cc_start: 0.8521 (ptpt) cc_final: 0.8202 (tmtm) outliers start: 51 outliers final: 28 residues processed: 373 average time/residue: 0.5531 time to fit residues: 230.8787 Evaluate side-chains 364 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 330 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 470 MET Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 490 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 80 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 149 optimal weight: 0.4980 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 146 optimal weight: 0.4980 chunk 78 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN E 147 GLN E 213 GLN K 471 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.111971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.073991 restraints weight = 157779.507| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 5.05 r_work: 0.2684 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 17337 Z= 0.153 Angle : 0.661 13.427 23698 Z= 0.325 Chirality : 0.046 0.409 2695 Planarity : 0.004 0.062 2896 Dihedral : 10.163 113.488 2929 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.47 % Allowed : 21.32 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % 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: 1.53 (0.19), residues: 2027 helix: 1.60 (0.21), residues: 602 sheet: 1.19 (0.21), residues: 579 loop : 0.60 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 459 TYR 0.023 0.002 TYR E 318 PHE 0.028 0.002 PHE A 433 TRP 0.027 0.001 TRP B 237 HIS 0.004 0.001 HIS E 240 Details of bonding type rmsd covalent geometry : bond 0.00347 (17300) covalent geometry : angle 0.64994 (23595) SS BOND : bond 0.00156 ( 8) SS BOND : angle 0.51379 ( 16) hydrogen bonds : bond 0.03768 ( 838) hydrogen bonds : angle 4.49118 ( 2660) link_ALPHA1-3 : bond 0.00992 ( 4) link_ALPHA1-3 : angle 2.04104 ( 12) link_ALPHA1-6 : bond 0.00888 ( 4) link_ALPHA1-6 : angle 1.63613 ( 12) link_BETA1-4 : bond 0.00293 ( 12) link_BETA1-4 : angle 1.63463 ( 36) link_NAG-ASN : bond 0.00496 ( 9) link_NAG-ASN : angle 2.69375 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 348 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6888 (mmm) cc_final: 0.6563 (tpt) REVERT: A 13 LYS cc_start: 0.8657 (mtpp) cc_final: 0.8023 (mttp) REVERT: A 137 MET cc_start: 0.8494 (tpp) cc_final: 0.8147 (ptt) REVERT: A 141 ARG cc_start: 0.8358 (mtm-85) cc_final: 0.8028 (mpt180) REVERT: A 244 TYR cc_start: 0.8164 (p90) cc_final: 0.7850 (p90) REVERT: A 426 TRP cc_start: 0.8067 (m-90) cc_final: 0.7518 (m-10) REVERT: B 261 MET cc_start: 0.9122 (mmp) cc_final: 0.8917 (mmp) REVERT: C 13 LYS cc_start: 0.8948 (tttt) cc_final: 0.8727 (tttm) REVERT: C 49 MET cc_start: 0.8408 (tmm) cc_final: 0.8170 (pp-130) REVERT: C 61 MET cc_start: 0.9423 (ptt) cc_final: 0.9181 (ptt) REVERT: C 141 ARG cc_start: 0.8785 (mtt90) cc_final: 0.8484 (mtm180) REVERT: C 235 LEU cc_start: 0.8760 (tp) cc_final: 0.8541 (tt) REVERT: C 244 TYR cc_start: 0.8398 (p90) cc_final: 0.8137 (p90) REVERT: C 274 LYS cc_start: 0.8125 (mttt) cc_final: 0.7810 (mmmm) REVERT: C 434 THR cc_start: 0.9120 (m) cc_final: 0.8872 (p) REVERT: D 9 MET cc_start: 0.7210 (ptp) cc_final: 0.6887 (ptt) REVERT: D 182 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7807 (mp0) REVERT: D 215 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8711 (ttpp) REVERT: D 218 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6663 (mm) REVERT: D 243 ASN cc_start: 0.8487 (t0) cc_final: 0.7890 (t0) REVERT: D 274 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8191 (mmmm) REVERT: D 306 PHE cc_start: 0.8278 (t80) cc_final: 0.7733 (t80) REVERT: D 425 ARG cc_start: 0.8173 (ppt170) cc_final: 0.7940 (ppt170) REVERT: E 118 LYS cc_start: 0.9129 (mtmm) cc_final: 0.8880 (mtmm) REVERT: E 208 LYS cc_start: 0.8933 (mttm) cc_final: 0.8587 (mtpt) REVERT: E 330 PHE cc_start: 0.7867 (t80) cc_final: 0.7574 (t80) REVERT: K 426 GLN cc_start: 0.7395 (pt0) cc_final: 0.6900 (pt0) REVERT: K 447 TYR cc_start: 0.9065 (m-80) cc_final: 0.8751 (m-80) REVERT: K 456 THR cc_start: 0.8200 (t) cc_final: 0.7859 (t) REVERT: K 469 GLU cc_start: 0.8169 (mp0) cc_final: 0.7842 (mp0) REVERT: K 470 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.7168 (mpt) REVERT: K 482 TYR cc_start: 0.9045 (m-80) cc_final: 0.8442 (m-80) REVERT: K 504 GLN cc_start: 0.8408 (mp10) cc_final: 0.7828 (pm20) REVERT: L 414 HIS cc_start: 0.8897 (m170) cc_final: 0.8498 (m170) REVERT: L 469 GLU cc_start: 0.8203 (mp0) cc_final: 0.7818 (mp0) REVERT: L 470 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7224 (mpt) REVERT: M 426 GLN cc_start: 0.8406 (tt0) cc_final: 0.7555 (tp40) REVERT: M 433 GLU cc_start: 0.8237 (tt0) cc_final: 0.8026 (pt0) REVERT: M 466 VAL cc_start: 0.8252 (t) cc_final: 0.7869 (p) outliers start: 39 outliers final: 23 residues processed: 364 average time/residue: 0.5312 time to fit residues: 217.1758 Evaluate side-chains 365 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 337 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain K residue 430 LYS Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 470 MET Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 470 MET Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 449 ASP Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 490 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 0.0770 chunk 164 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 187 optimal weight: 0.4980 chunk 126 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 27 optimal weight: 0.1980 chunk 189 optimal weight: 9.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN A 224 GLN B 185 GLN C 64 GLN E 147 GLN E 213 GLN K 471 ASN M 464 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.113085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.075531 restraints weight = 161938.752| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 5.07 r_work: 0.2713 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17337 Z= 0.122 Angle : 0.662 15.152 23698 Z= 0.324 Chirality : 0.046 0.394 2695 Planarity : 0.004 0.061 2896 Dihedral : 9.970 112.894 2929 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.96 % Allowed : 22.05 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % 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: 1.58 (0.19), residues: 2027 helix: 1.58 (0.21), residues: 602 sheet: 1.22 (0.21), residues: 578 loop : 0.70 (0.23), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 142 TYR 0.023 0.001 TYR E 318 PHE 0.029 0.001 PHE A 433 TRP 0.035 0.001 TRP B 237 HIS 0.003 0.001 HIS L 414 Details of bonding type rmsd covalent geometry : bond 0.00269 (17300) covalent geometry : angle 0.65289 (23595) SS BOND : bond 0.00136 ( 8) SS BOND : angle 0.34323 ( 16) hydrogen bonds : bond 0.03665 ( 838) hydrogen bonds : angle 4.40581 ( 2660) link_ALPHA1-3 : bond 0.01059 ( 4) link_ALPHA1-3 : angle 1.93946 ( 12) link_ALPHA1-6 : bond 0.00985 ( 4) link_ALPHA1-6 : angle 1.57330 ( 12) link_BETA1-4 : bond 0.00354 ( 12) link_BETA1-4 : angle 1.46083 ( 36) link_NAG-ASN : bond 0.00504 ( 9) link_NAG-ASN : angle 2.52366 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 346 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6883 (mmm) cc_final: 0.6555 (tpt) REVERT: A 13 LYS cc_start: 0.8661 (mtpp) cc_final: 0.8024 (mttp) REVERT: A 137 MET cc_start: 0.8437 (tpp) cc_final: 0.8094 (ptt) REVERT: A 141 ARG cc_start: 0.8339 (mtm-85) cc_final: 0.8026 (mpt180) REVERT: A 244 TYR cc_start: 0.8140 (p90) cc_final: 0.7869 (p90) REVERT: A 306 PHE cc_start: 0.8068 (t80) cc_final: 0.7832 (t80) REVERT: A 426 TRP cc_start: 0.8045 (m-90) cc_final: 0.7501 (m-10) REVERT: C 13 LYS cc_start: 0.8967 (tttt) cc_final: 0.8749 (tttm) REVERT: C 49 MET cc_start: 0.8451 (tmm) cc_final: 0.8220 (pp-130) REVERT: C 61 MET cc_start: 0.9401 (ptt) cc_final: 0.9175 (ptt) REVERT: C 141 ARG cc_start: 0.8788 (mtt90) cc_final: 0.8506 (mtm180) REVERT: C 235 LEU cc_start: 0.8746 (tp) cc_final: 0.8533 (tt) REVERT: C 244 TYR cc_start: 0.8373 (p90) cc_final: 0.8140 (p90) REVERT: C 274 LYS cc_start: 0.8102 (mttt) cc_final: 0.7572 (mmmm) REVERT: C 434 THR cc_start: 0.9132 (m) cc_final: 0.8885 (p) REVERT: D 9 MET cc_start: 0.7226 (ptp) cc_final: 0.6893 (ptt) REVERT: D 182 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7800 (mp0) REVERT: D 215 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8730 (ttpp) REVERT: D 218 ILE cc_start: 0.7177 (OUTLIER) cc_final: 0.6672 (mm) REVERT: D 227 MET cc_start: 0.7591 (tpp) cc_final: 0.6708 (tmm) REVERT: D 243 ASN cc_start: 0.8481 (t0) cc_final: 0.7859 (t0) REVERT: D 274 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8154 (mmmm) REVERT: D 306 PHE cc_start: 0.8231 (t80) cc_final: 0.7751 (t80) REVERT: D 425 ARG cc_start: 0.8160 (ppt170) cc_final: 0.7930 (ppt170) REVERT: E 118 LYS cc_start: 0.9133 (mtmm) cc_final: 0.8880 (mtmm) REVERT: E 208 LYS cc_start: 0.8930 (mttm) cc_final: 0.8591 (mtpt) REVERT: E 330 PHE cc_start: 0.7786 (t80) cc_final: 0.7479 (t80) REVERT: K 426 GLN cc_start: 0.7374 (pt0) cc_final: 0.6780 (pt0) REVERT: K 447 TYR cc_start: 0.9022 (m-80) cc_final: 0.8721 (m-80) REVERT: K 456 THR cc_start: 0.8230 (t) cc_final: 0.8000 (t) REVERT: K 468 LEU cc_start: 0.7815 (tp) cc_final: 0.7491 (pt) REVERT: K 469 GLU cc_start: 0.8040 (mp0) cc_final: 0.7755 (mp0) REVERT: K 482 TYR cc_start: 0.9035 (m-80) cc_final: 0.8365 (m-80) REVERT: K 504 GLN cc_start: 0.8462 (mp10) cc_final: 0.7887 (pm20) REVERT: L 1 GLN cc_start: 0.8195 (pm20) cc_final: 0.7964 (pm20) REVERT: L 463 LYS cc_start: 0.8630 (mmtt) cc_final: 0.8220 (mtmm) REVERT: L 469 GLU cc_start: 0.8157 (mp0) cc_final: 0.7804 (mp0) REVERT: L 470 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7082 (mpt) REVERT: M 426 GLN cc_start: 0.8415 (tt0) cc_final: 0.7580 (tp40) REVERT: M 466 VAL cc_start: 0.8229 (t) cc_final: 0.7827 (p) REVERT: M 474 LYS cc_start: 0.8511 (ptpt) cc_final: 0.8220 (tmtm) outliers start: 29 outliers final: 19 residues processed: 359 average time/residue: 0.5183 time to fit residues: 209.0153 Evaluate side-chains 356 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 333 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 470 MET Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 490 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 45 optimal weight: 0.9990 chunk 192 optimal weight: 0.0270 chunk 152 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 193 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 40 optimal weight: 0.3980 chunk 90 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN E 147 GLN E 213 GLN K 471 ASN L 414 HIS M 464 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.112581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.075299 restraints weight = 147053.895| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 4.87 r_work: 0.2715 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17337 Z= 0.140 Angle : 0.664 13.455 23698 Z= 0.328 Chirality : 0.046 0.386 2695 Planarity : 0.004 0.061 2896 Dihedral : 9.923 112.748 2929 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.96 % Allowed : 22.73 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % 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: 1.55 (0.19), residues: 2027 helix: 1.48 (0.21), residues: 602 sheet: 1.24 (0.22), residues: 579 loop : 0.70 (0.23), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 207 TYR 0.024 0.002 TYR E 318 PHE 0.036 0.002 PHE L 455 TRP 0.039 0.001 TRP B 237 HIS 0.004 0.001 HIS L 414 Details of bonding type rmsd covalent geometry : bond 0.00320 (17300) covalent geometry : angle 0.65465 (23595) SS BOND : bond 0.00147 ( 8) SS BOND : angle 0.41260 ( 16) hydrogen bonds : bond 0.03659 ( 838) hydrogen bonds : angle 4.42362 ( 2660) link_ALPHA1-3 : bond 0.00989 ( 4) link_ALPHA1-3 : angle 1.98665 ( 12) link_ALPHA1-6 : bond 0.00957 ( 4) link_ALPHA1-6 : angle 1.58450 ( 12) link_BETA1-4 : bond 0.00328 ( 12) link_BETA1-4 : angle 1.52621 ( 36) link_NAG-ASN : bond 0.00498 ( 9) link_NAG-ASN : angle 2.52418 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6804.20 seconds wall clock time: 116 minutes 29.77 seconds (6989.77 seconds total)