Starting phenix.real_space_refine on Wed Mar 4 22:54:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qnd_14075/03_2026/7qnd_14075.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qnd_14075/03_2026/7qnd_14075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qnd_14075/03_2026/7qnd_14075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qnd_14075/03_2026/7qnd_14075.map" model { file = "/net/cci-nas-00/data/ceres_data/7qnd_14075/03_2026/7qnd_14075.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qnd_14075/03_2026/7qnd_14075.cif" } resolution = 3.4 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 89 5.16 5 C 10938 2.51 5 N 2705 2.21 5 O 3078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16810 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2744 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: 2689 Chain: "B" 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: 2662 Chain: "C" Number of atoms: 2760 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: 2669 Chain: "D" Number of atoms: 2725 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: 2710 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: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'HSM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'EI7': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 12 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 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: 6.12, per 1000 atoms: 0.36 Number of scatterers: 16810 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 89 16.00 O 3078 8.00 N 2705 7.00 C 10938 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 502 " - " 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: 1.51 Conformation dependent library (CDL) restraints added in 1.1 seconds 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3814 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 25 sheets defined 35.4% alpha, 41.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 removed outlier: 3.938A pdb=" N PHE A 11 " --> pdb=" O GLY A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 84 through 91 removed outlier: 3.547A 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: 3.646A pdb=" N LEU A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 242 removed outlier: 3.633A pdb=" N VAL A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 271 removed outlier: 3.592A 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 447 removed outlier: 3.637A 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: 3.547A 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: 3.646A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 242 removed outlier: 3.633A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 271 removed outlier: 3.592A 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 447 removed outlier: 3.637A 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: 3.547A 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: 3.646A pdb=" N LEU C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 242 removed outlier: 3.633A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 271 removed outlier: 3.592A 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 447 removed outlier: 3.637A 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: 3.547A 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: 3.647A pdb=" N LEU D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 242 removed outlier: 3.633A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 271 removed outlier: 3.592A 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 447 removed outlier: 3.638A 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 removed outlier: 3.651A pdb=" N GLY E 50 " --> pdb=" O GLY E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 101 Processing helix chain 'E' and resid 112 through 119 removed outlier: 3.771A 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: 3.557A pdb=" N ILE E 252 " --> pdb=" O GLY E 248 " (cutoff:3.500A) Proline residue: E 257 - end of helix removed outlier: 4.046A 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: 4.098A pdb=" N TRP E 270 " --> pdb=" O TRP E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 300 Processing helix chain 'E' and resid 308 through 336 removed outlier: 3.517A pdb=" N LEU E 325 " --> pdb=" O VAL E 321 " (cutoff:3.500A) 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: 4.420A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.613A 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: 6.687A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N THR A 176 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE A 42 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.821A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU A 190 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.889A 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: 4.420A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.613A 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: 6.687A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N THR B 176 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE B 42 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.821A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.888A 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: 4.420A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.613A 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: 6.687A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N THR C 176 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE C 42 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.822A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.888A 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: 4.419A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.612A 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: 6.687A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N VAL D 106 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ARG D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N THR D 176 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE D 42 " --> pdb=" O THR D 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.821A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.888A 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: 3.745A pdb=" N ILE E 144 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ALA E 163 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 6.117A 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: 3.745A pdb=" N ILE E 144 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLU E 84 " --> pdb=" O HIS E 77 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N HIS E 77 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR E 86 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE E 75 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR E 88 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ARG E 96 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN E 65 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL E 64 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N TYR E 195 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 6.307A 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: 4.427A pdb=" N SER E 184 " --> pdb=" O PRO E 235 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 124 through 126 removed outlier: 4.427A pdb=" N SER E 184 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE E 234 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N MET E 226 " --> pdb=" O PHE E 234 " (cutoff:3.500A) removed outlier: 4.005A 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: 5.678A pdb=" N ILE E 216 " --> pdb=" O ARG E 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 2 through 7 Processing sheet with id=AB9, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.756A pdb=" N GLY K 10 " --> pdb=" O THR K 509 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL K 508 " --> pdb=" O ALA K 479 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL K 480 " --> pdb=" O GLN K 426 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE K 420 " --> pdb=" O LYS K 486 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET K 421 " --> pdb=" O ALA K 437 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA K 437 " --> pdb=" O MET K 421 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP K 423 " --> pdb=" O VAL K 435 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.756A pdb=" N GLY K 10 " --> pdb=" O THR K 509 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL K 508 " --> pdb=" O ALA K 479 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR K 501 " --> pdb=" O ALA K 485 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 2 through 7 Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.756A pdb=" N GLY L 10 " --> pdb=" O THR L 509 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL L 508 " --> pdb=" O ALA L 479 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL L 480 " --> pdb=" O GLN L 426 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE L 420 " --> pdb=" O LYS L 486 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET L 421 " --> pdb=" O ALA L 437 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA L 437 " --> pdb=" O MET L 421 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP L 423 " --> pdb=" O VAL L 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.756A pdb=" N GLY L 10 " --> pdb=" O THR L 509 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL L 508 " --> pdb=" O ALA L 479 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR L 501 " --> pdb=" O ALA L 485 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 2 through 7 Processing sheet with id=AC6, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.756A pdb=" N GLY M 10 " --> pdb=" O THR M 509 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL M 508 " --> pdb=" O ALA M 479 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL M 480 " --> pdb=" O GLN M 426 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET M 421 " --> pdb=" O ALA M 437 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA M 437 " --> pdb=" O MET M 421 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP M 423 " --> pdb=" O VAL M 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.756A pdb=" N GLY M 10 " --> pdb=" O THR M 509 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL M 508 " --> pdb=" O ALA M 479 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR M 501 " --> pdb=" O ALA M 485 " (cutoff:3.500A) 930 hydrogen bonds defined for protein. 2623 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: 3.43 Time building geometry restraints manager: 2.01 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: 5110 1.34 - 1.46: 4432 1.46 - 1.58: 7596 1.58 - 1.69: 0 1.69 - 1.81: 153 Bond restraints: 17291 Sorted by residual: bond pdb=" N EI7 E 501 " pdb=" C EI7 E 501 " ideal model delta sigma weight residual 1.388 1.457 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C EI7 E 501 " pdb=" C2 EI7 E 501 " ideal model delta sigma weight residual 1.446 1.477 -0.031 2.00e-02 2.50e+03 2.42e+00 bond pdb=" C1 MAN F 5 " pdb=" O5 MAN F 5 " ideal model delta sigma weight residual 1.399 1.429 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C1 MAN G 5 " pdb=" O5 MAN G 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 MAN I 5 " pdb=" O5 MAN I 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.10e+00 ... (remaining 17286 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 23044 1.24 - 2.47: 354 2.47 - 3.71: 148 3.71 - 4.95: 24 4.95 - 6.19: 7 Bond angle restraints: 23577 Sorted by residual: angle pdb=" N EI7 E 501 " pdb=" C EI7 E 501 " pdb=" O EI7 E 501 " ideal model delta sigma weight residual 124.11 130.30 -6.19 3.00e+00 1.11e-01 4.25e+00 angle pdb=" CA ATYR D 66 " pdb=" CB ATYR D 66 " pdb=" CG ATYR D 66 " ideal model delta sigma weight residual 113.90 117.21 -3.31 1.80e+00 3.09e-01 3.39e+00 angle pdb=" C1 BMA F 3 " pdb=" O5 BMA F 3 " pdb=" C5 BMA F 3 " ideal model delta sigma weight residual 118.82 113.40 5.42 3.00e+00 1.11e-01 3.27e+00 angle pdb=" C1 BMA H 3 " pdb=" O5 BMA H 3 " pdb=" C5 BMA H 3 " ideal model delta sigma weight residual 118.82 113.44 5.38 3.00e+00 1.11e-01 3.21e+00 angle pdb=" C1 BMA G 3 " pdb=" O5 BMA G 3 " pdb=" C5 BMA G 3 " ideal model delta sigma weight residual 118.82 113.51 5.31 3.00e+00 1.11e-01 3.13e+00 ... (remaining 23572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.14: 10283 21.14 - 42.29: 144 42.29 - 63.43: 14 63.43 - 84.57: 31 84.57 - 105.72: 16 Dihedral angle restraints: 10488 sinusoidal: 4484 harmonic: 6004 Sorted by residual: dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.01 105.72 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" O4 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C5 BMA H 3 " pdb=" O5 BMA H 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.71 105.42 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O4 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.50 105.21 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 10485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2269 0.052 - 0.105: 358 0.105 - 0.157: 51 0.157 - 0.210: 9 0.210 - 0.262: 4 Chirality restraints: 2691 Sorted by residual: 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 -2.29 -0.11 2.00e-02 2.50e+03 2.88e+01 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 2.30 0.10 2.00e-02 2.50e+03 2.71e+01 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.02e+01 ... (remaining 2688 not shown) Planarity restraints: 2909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 435 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO E 436 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO E 436 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 436 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 171 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO E 172 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO E 172 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 172 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ATYR D 66 " 0.009 2.00e-02 2.50e+03 6.80e-03 9.24e-01 pdb=" CG ATYR D 66 " -0.016 2.00e-02 2.50e+03 pdb=" CD1ATYR D 66 " 0.003 2.00e-02 2.50e+03 pdb=" CD2ATYR D 66 " -0.000 2.00e-02 2.50e+03 pdb=" CE1ATYR D 66 " 0.000 2.00e-02 2.50e+03 pdb=" CE2ATYR D 66 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ATYR D 66 " -0.000 2.00e-02 2.50e+03 pdb=" OH ATYR D 66 " 0.000 2.00e-02 2.50e+03 ... (remaining 2906 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1495 2.75 - 3.29: 16373 3.29 - 3.82: 28914 3.82 - 4.36: 35628 4.36 - 4.90: 60640 Nonbonded interactions: 143050 Sorted by model distance: nonbonded pdb=" OH TYR E 171 " pdb=" OH TYR E 250 " model vdw 2.210 3.040 nonbonded pdb=" ND2AASN A 41 " pdb=" O ARG A 169 " model vdw 2.249 3.120 nonbonded pdb=" ND2AASN B 41 " pdb=" O ARG B 169 " model vdw 2.312 3.120 nonbonded pdb=" ND2AASN C 41 " pdb=" O ARG C 169 " model vdw 2.318 3.120 nonbonded pdb=" OD2 ASP C 146 " pdb=" NE2 GLN C 148 " model vdw 2.337 3.120 ... (remaining 143045 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 425 or resid 427 thro \ ugh 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 425 or resid 427 thro \ ugh 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 425 or resid 427 thro \ ugh 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 425 or resid 427 thro \ ugh 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 19.750 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 0.069 17328 Z= 0.126 Angle : 0.461 6.187 23680 Z= 0.208 Chirality : 0.042 0.262 2691 Planarity : 0.003 0.033 2900 Dihedral : 10.267 105.716 6650 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.45 % Allowed : 1.68 % Favored : 97.87 % 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: 2.54 (0.20), residues: 2024 helix: 2.97 (0.21), residues: 553 sheet: 1.52 (0.22), residues: 656 loop : 1.04 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 213 TYR 0.008 0.001 TYR B 126 PHE 0.007 0.001 PHE E 90 TRP 0.005 0.001 TRP C 67 HIS 0.001 0.000 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00260 (17291) covalent geometry : angle 0.45770 (23577) SS BOND : bond 0.00054 ( 8) SS BOND : angle 0.40503 ( 16) hydrogen bonds : bond 0.22291 ( 826) hydrogen bonds : angle 7.19371 ( 2623) link_ALPHA1-3 : bond 0.00114 ( 4) link_ALPHA1-3 : angle 0.91731 ( 12) link_ALPHA1-6 : bond 0.00038 ( 4) link_ALPHA1-6 : angle 0.90757 ( 12) link_BETA1-4 : bond 0.00119 ( 12) link_BETA1-4 : angle 1.07298 ( 36) link_NAG-ASN : bond 0.00122 ( 9) link_NAG-ASN : angle 1.07846 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 602 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6735 (mtp) cc_final: 0.6045 (mpp) REVERT: A 85 ASN cc_start: 0.7088 (p0) cc_final: 0.6873 (p0) REVERT: A 151 THR cc_start: 0.8574 (p) cc_final: 0.8265 (p) REVERT: A 192 ARG cc_start: 0.7490 (mtt180) cc_final: 0.6944 (mtt180) REVERT: A 229 SER cc_start: 0.9333 (m) cc_final: 0.9055 (t) REVERT: A 268 LEU cc_start: 0.8589 (tp) cc_final: 0.8358 (tp) REVERT: A 284 TYR cc_start: 0.8394 (t80) cc_final: 0.8192 (t80) REVERT: A 288 CYS cc_start: 0.9209 (m) cc_final: 0.8728 (m) REVERT: A 429 ILE cc_start: 0.9032 (tp) cc_final: 0.8701 (mm) REVERT: A 445 TYR cc_start: 0.7920 (t80) cc_final: 0.7668 (t80) REVERT: A 446 TYR cc_start: 0.8103 (m-80) cc_final: 0.7812 (m-80) REVERT: B 272 LEU cc_start: 0.9018 (mt) cc_final: 0.8803 (mt) REVERT: B 298 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7838 (tm-30) REVERT: B 301 PHE cc_start: 0.8107 (t80) cc_final: 0.7887 (t80) REVERT: B 425 ARG cc_start: 0.8642 (ttt180) cc_final: 0.8186 (mtt180) REVERT: B 433 PHE cc_start: 0.8830 (t80) cc_final: 0.8599 (t80) REVERT: C 52 GLU cc_start: 0.8018 (mp0) cc_final: 0.7727 (mm-30) REVERT: C 95 ASP cc_start: 0.8348 (p0) cc_final: 0.8131 (p0) REVERT: C 138 MET cc_start: 0.8699 (mtt) cc_final: 0.8001 (mtt) REVERT: C 141 ARG cc_start: 0.7974 (mtt90) cc_final: 0.7665 (mtm-85) REVERT: C 243 ASN cc_start: 0.7510 (t0) cc_final: 0.6833 (p0) REVERT: C 250 ARG cc_start: 0.8430 (mtp180) cc_final: 0.8167 (mtp180) REVERT: C 274 LYS cc_start: 0.8927 (mttt) cc_final: 0.8713 (mtmt) REVERT: D 223 LEU cc_start: 0.8990 (mt) cc_final: 0.8477 (pp) REVERT: D 227 MET cc_start: 0.8341 (mmt) cc_final: 0.8076 (tpp) REVERT: D 243 ASN cc_start: 0.7359 (t0) cc_final: 0.6725 (t0) REVERT: D 268 LEU cc_start: 0.8021 (tp) cc_final: 0.7418 (tp) REVERT: D 270 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7917 (mm-30) REVERT: D 306 PHE cc_start: 0.7943 (t80) cc_final: 0.7023 (t80) REVERT: D 425 ARG cc_start: 0.8963 (ttt180) cc_final: 0.8710 (ttm170) REVERT: D 437 LEU cc_start: 0.9187 (tp) cc_final: 0.8971 (mm) REVERT: E 142 LYS cc_start: 0.8951 (mttt) cc_final: 0.8567 (mttm) REVERT: E 222 THR cc_start: 0.8717 (m) cc_final: 0.8456 (p) REVERT: E 290 MET cc_start: 0.8589 (tpp) cc_final: 0.8121 (tmm) REVERT: E 317 CYS cc_start: 0.9008 (m) cc_final: 0.8803 (m) REVERT: E 332 HIS cc_start: 0.8807 (t70) cc_final: 0.8591 (t70) REVERT: K 460 ASP cc_start: 0.7492 (p0) cc_final: 0.7201 (p0) REVERT: K 509 THR cc_start: 0.8012 (m) cc_final: 0.7448 (p) REVERT: L 459 ARG cc_start: 0.8121 (pmt-80) cc_final: 0.7488 (ppt170) REVERT: L 460 ASP cc_start: 0.7239 (p0) cc_final: 0.6834 (p0) REVERT: L 474 LYS cc_start: 0.8873 (mttt) cc_final: 0.8639 (ttpt) REVERT: L 501 TYR cc_start: 0.8355 (m-80) cc_final: 0.7982 (m-80) REVERT: M 455 PHE cc_start: 0.7613 (m-10) cc_final: 0.7008 (m-10) REVERT: M 464 ASN cc_start: 0.8391 (m-40) cc_final: 0.8189 (m-40) REVERT: M 465 THR cc_start: 0.8517 (m) cc_final: 0.8302 (p) REVERT: M 481 TYR cc_start: 0.8538 (m-80) cc_final: 0.8011 (m-10) REVERT: M 482 TYR cc_start: 0.8024 (m-80) cc_final: 0.7756 (m-80) REVERT: M 509 THR cc_start: 0.8695 (m) cc_final: 0.8366 (t) outliers start: 8 outliers final: 0 residues processed: 608 average time/residue: 0.1567 time to fit residues: 138.6899 Evaluate side-chains 378 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN C 65 GLN C 265 ASN E 147 GLN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.097426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.069512 restraints weight = 280329.220| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 8.24 r_work: 0.2834 rms_B_bonded: 6.87 restraints_weight: 2.0000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17328 Z= 0.144 Angle : 0.681 13.731 23680 Z= 0.340 Chirality : 0.045 0.221 2691 Planarity : 0.004 0.045 2900 Dihedral : 9.088 82.707 2920 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.02 % Allowed : 12.97 % Favored : 85.01 % 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: 2.23 (0.19), residues: 2024 helix: 2.48 (0.21), residues: 583 sheet: 1.33 (0.21), residues: 641 loop : 0.98 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 141 TYR 0.025 0.002 TYR D 284 PHE 0.019 0.002 PHE A 221 TRP 0.018 0.001 TRP D 237 HIS 0.003 0.000 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00309 (17291) covalent geometry : angle 0.67513 (23577) SS BOND : bond 0.00217 ( 8) SS BOND : angle 0.58005 ( 16) hydrogen bonds : bond 0.05371 ( 826) hydrogen bonds : angle 5.10891 ( 2623) link_ALPHA1-3 : bond 0.00911 ( 4) link_ALPHA1-3 : angle 2.33103 ( 12) link_ALPHA1-6 : bond 0.00892 ( 4) link_ALPHA1-6 : angle 1.84247 ( 12) link_BETA1-4 : bond 0.00291 ( 12) link_BETA1-4 : angle 1.54222 ( 36) link_NAG-ASN : bond 0.00143 ( 9) link_NAG-ASN : angle 1.21971 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 408 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 TYR cc_start: 0.8393 (m-80) cc_final: 0.8121 (m-80) REVERT: A 89 ASP cc_start: 0.9205 (t0) cc_final: 0.8887 (p0) REVERT: A 141 ARG cc_start: 0.8439 (mtt90) cc_final: 0.8136 (mtt90) REVERT: A 429 ILE cc_start: 0.9007 (tp) cc_final: 0.8729 (mm) REVERT: B 18 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8871 (mtmt) REVERT: B 55 MET cc_start: 0.9084 (mmm) cc_final: 0.8508 (mmm) REVERT: B 90 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7930 (mp10) REVERT: B 306 PHE cc_start: 0.8389 (t80) cc_final: 0.7964 (t80) REVERT: B 425 ARG cc_start: 0.8618 (ttt180) cc_final: 0.8109 (mtt180) REVERT: C 18 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8569 (ptpp) REVERT: C 49 MET cc_start: 0.9067 (ttp) cc_final: 0.8721 (tmm) REVERT: C 55 MET cc_start: 0.9331 (mmt) cc_final: 0.8605 (mmt) REVERT: C 141 ARG cc_start: 0.8604 (mtt90) cc_final: 0.8154 (mtm-85) REVERT: C 226 TYR cc_start: 0.9143 (m-80) cc_final: 0.8896 (m-80) REVERT: C 267 HIS cc_start: 0.8313 (m90) cc_final: 0.8112 (m90) REVERT: C 270 GLU cc_start: 0.8043 (pt0) cc_final: 0.7805 (pp20) REVERT: C 277 TYR cc_start: 0.8160 (p90) cc_final: 0.7390 (p90) REVERT: C 286 MET cc_start: 0.8558 (mmm) cc_final: 0.7912 (ttp) REVERT: D 14 GLU cc_start: 0.8852 (pt0) cc_final: 0.8606 (pp20) REVERT: D 18 LYS cc_start: 0.9089 (mtmm) cc_final: 0.8803 (mtmm) REVERT: D 55 MET cc_start: 0.9141 (mmt) cc_final: 0.8561 (mmt) REVERT: D 79 LEU cc_start: 0.9208 (mp) cc_final: 0.8861 (tp) REVERT: D 165 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8536 (mp0) REVERT: D 220 TYR cc_start: 0.8613 (t80) cc_final: 0.8254 (t80) REVERT: D 223 LEU cc_start: 0.8979 (mt) cc_final: 0.8556 (pp) REVERT: D 227 MET cc_start: 0.8652 (mmt) cc_final: 0.8356 (tpp) REVERT: D 243 ASN cc_start: 0.7329 (t0) cc_final: 0.6967 (t0) REVERT: D 270 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7922 (mm-30) REVERT: D 425 ARG cc_start: 0.8943 (ttt180) cc_final: 0.8691 (ttm170) REVERT: E 327 GLU cc_start: 0.9222 (tm-30) cc_final: 0.8879 (tm-30) REVERT: E 332 HIS cc_start: 0.8841 (t70) cc_final: 0.8631 (t70) REVERT: K 456 THR cc_start: 0.7918 (p) cc_final: 0.7690 (p) REVERT: K 469 GLU cc_start: 0.6827 (mp0) cc_final: 0.5995 (mp0) REVERT: L 459 ARG cc_start: 0.8272 (pmt-80) cc_final: 0.7827 (ppt170) REVERT: M 3 GLN cc_start: 0.8474 (mp10) cc_final: 0.8218 (pm20) REVERT: M 452 LYS cc_start: 0.9091 (mtpt) cc_final: 0.8805 (mttm) REVERT: M 464 ASN cc_start: 0.8819 (m-40) cc_final: 0.8606 (m-40) REVERT: M 469 GLU cc_start: 0.8143 (mp0) cc_final: 0.7877 (mp0) REVERT: M 474 LYS cc_start: 0.8980 (mttt) cc_final: 0.8649 (mtmm) outliers start: 36 outliers final: 19 residues processed: 424 average time/residue: 0.1385 time to fit residues: 89.0880 Evaluate side-chains 375 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 353 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain L residue 449 ASP Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain M residue 445 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 80 optimal weight: 3.9990 chunk 106 optimal weight: 0.0570 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 105 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A C 265 ASN E 82 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 472 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.095227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.066496 restraints weight = 246543.030| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 7.94 r_work: 0.2747 rms_B_bonded: 6.69 restraints_weight: 2.0000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17328 Z= 0.178 Angle : 0.638 11.092 23680 Z= 0.323 Chirality : 0.045 0.202 2691 Planarity : 0.004 0.043 2900 Dihedral : 8.634 77.316 2920 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.25 % Allowed : 14.21 % Favored : 83.55 % 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: 1.95 (0.19), residues: 2024 helix: 2.24 (0.21), residues: 585 sheet: 1.11 (0.20), residues: 648 loop : 0.89 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 86 TYR 0.023 0.002 TYR A 445 PHE 0.020 0.002 PHE D 63 TRP 0.023 0.001 TRP D 237 HIS 0.003 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00397 (17291) covalent geometry : angle 0.63286 (23577) SS BOND : bond 0.00170 ( 8) SS BOND : angle 0.40686 ( 16) hydrogen bonds : bond 0.04712 ( 826) hydrogen bonds : angle 4.83415 ( 2623) link_ALPHA1-3 : bond 0.00920 ( 4) link_ALPHA1-3 : angle 1.91867 ( 12) link_ALPHA1-6 : bond 0.00733 ( 4) link_ALPHA1-6 : angle 1.75091 ( 12) link_BETA1-4 : bond 0.00314 ( 12) link_BETA1-4 : angle 1.55152 ( 36) link_NAG-ASN : bond 0.00142 ( 9) link_NAG-ASN : angle 1.15359 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 361 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6837 (mtp) cc_final: 0.5872 (mpp) REVERT: A 66 TYR cc_start: 0.8497 (m-80) cc_final: 0.8197 (m-80) REVERT: A 227 MET cc_start: 0.8622 (ttt) cc_final: 0.8270 (ttp) REVERT: A 429 ILE cc_start: 0.8984 (tp) cc_final: 0.8710 (mm) REVERT: A 445 TYR cc_start: 0.8131 (t80) cc_final: 0.7914 (t80) REVERT: B 18 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.9043 (mtmt) REVERT: B 55 MET cc_start: 0.9148 (mmm) cc_final: 0.8379 (mmm) REVERT: B 306 PHE cc_start: 0.8285 (t80) cc_final: 0.7989 (t80) REVERT: C 18 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8630 (ptpp) REVERT: C 52 GLU cc_start: 0.8888 (mp0) cc_final: 0.8554 (mm-30) REVERT: C 55 MET cc_start: 0.9350 (mmt) cc_final: 0.8738 (mmt) REVERT: C 95 ASP cc_start: 0.9180 (p0) cc_final: 0.8880 (p0) REVERT: C 141 ARG cc_start: 0.8681 (mtt90) cc_final: 0.8175 (mtm-85) REVERT: C 226 TYR cc_start: 0.9280 (m-80) cc_final: 0.9040 (m-80) REVERT: C 267 HIS cc_start: 0.8414 (m90) cc_final: 0.8176 (m90) REVERT: C 270 GLU cc_start: 0.8034 (pt0) cc_final: 0.7759 (pp20) REVERT: C 298 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8453 (tm-30) REVERT: D 14 GLU cc_start: 0.8839 (pt0) cc_final: 0.8638 (pp20) REVERT: D 18 LYS cc_start: 0.9143 (mtmm) cc_final: 0.8875 (mtmm) REVERT: D 79 LEU cc_start: 0.9249 (mp) cc_final: 0.8963 (mm) REVERT: D 165 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8383 (mp0) REVERT: D 220 TYR cc_start: 0.8630 (t80) cc_final: 0.8297 (t80) REVERT: D 223 LEU cc_start: 0.8902 (mt) cc_final: 0.8533 (pp) REVERT: D 227 MET cc_start: 0.8674 (mmt) cc_final: 0.8295 (tpp) REVERT: D 243 ASN cc_start: 0.7053 (t0) cc_final: 0.6706 (t0) REVERT: D 270 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7886 (mm-30) REVERT: E 83 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8537 (mmm) REVERT: E 170 LYS cc_start: 0.8186 (mttt) cc_final: 0.7551 (mmmt) REVERT: E 255 TYR cc_start: 0.8148 (m-80) cc_final: 0.7846 (m-80) REVERT: E 290 MET cc_start: 0.8899 (mmm) cc_final: 0.8698 (mmm) REVERT: E 332 HIS cc_start: 0.8856 (t70) cc_final: 0.8635 (t70) REVERT: K 1 GLN cc_start: 0.8312 (pm20) cc_final: 0.7869 (pm20) REVERT: K 425 ARG cc_start: 0.7972 (ptp90) cc_final: 0.7478 (ptp90) REVERT: K 481 TYR cc_start: 0.7845 (m-80) cc_final: 0.7379 (m-80) REVERT: K 504 GLN cc_start: 0.8825 (mp10) cc_final: 0.8587 (pm20) REVERT: L 425 ARG cc_start: 0.8999 (ptt90) cc_final: 0.8591 (ptt-90) REVERT: L 433 GLU cc_start: 0.9261 (tp30) cc_final: 0.9049 (pt0) REVERT: L 459 ARG cc_start: 0.8255 (pmt-80) cc_final: 0.7777 (ppt170) REVERT: M 3 GLN cc_start: 0.8575 (mp10) cc_final: 0.8297 (pm20) REVERT: M 452 LYS cc_start: 0.9110 (mtpt) cc_final: 0.8803 (mttm) REVERT: M 464 ASN cc_start: 0.8760 (m-40) cc_final: 0.8555 (m-40) REVERT: M 469 GLU cc_start: 0.8223 (mp0) cc_final: 0.7896 (mp0) REVERT: M 474 LYS cc_start: 0.8999 (mttt) cc_final: 0.8622 (mtmm) REVERT: M 481 TYR cc_start: 0.8382 (m-10) cc_final: 0.7955 (m-10) outliers start: 40 outliers final: 31 residues processed: 381 average time/residue: 0.1414 time to fit residues: 81.9075 Evaluate side-chains 371 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 337 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 509 THR Chi-restraints excluded: chain L residue 449 ASP Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 504 GLN Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 445 THR Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 472 ASN Chi-restraints excluded: chain M residue 493 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 138 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 188 optimal weight: 0.8980 chunk 189 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 414 HIS L 504 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.093892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.065122 restraints weight = 242886.540| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 7.44 r_work: 0.2738 rms_B_bonded: 6.41 restraints_weight: 2.0000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17328 Z= 0.167 Angle : 0.631 11.523 23680 Z= 0.317 Chirality : 0.045 0.403 2691 Planarity : 0.003 0.035 2900 Dihedral : 8.123 70.263 2920 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.92 % Allowed : 14.32 % Favored : 82.76 % 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: 1.79 (0.19), residues: 2024 helix: 2.08 (0.21), residues: 585 sheet: 1.16 (0.21), residues: 590 loop : 0.71 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 114 TYR 0.024 0.002 TYR A 299 PHE 0.017 0.002 PHE D 63 TRP 0.022 0.001 TRP D 237 HIS 0.003 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00375 (17291) covalent geometry : angle 0.62539 (23577) SS BOND : bond 0.00133 ( 8) SS BOND : angle 0.33860 ( 16) hydrogen bonds : bond 0.04201 ( 826) hydrogen bonds : angle 4.66829 ( 2623) link_ALPHA1-3 : bond 0.00886 ( 4) link_ALPHA1-3 : angle 1.96184 ( 12) link_ALPHA1-6 : bond 0.00800 ( 4) link_ALPHA1-6 : angle 1.84253 ( 12) link_BETA1-4 : bond 0.00279 ( 12) link_BETA1-4 : angle 1.57231 ( 36) link_NAG-ASN : bond 0.00118 ( 9) link_NAG-ASN : angle 1.14679 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 347 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6690 (mtp) cc_final: 0.5834 (mpp) REVERT: A 49 MET cc_start: 0.8623 (ppp) cc_final: 0.8422 (ppp) REVERT: A 66 TYR cc_start: 0.8534 (m-80) cc_final: 0.8242 (m-80) REVERT: A 227 MET cc_start: 0.8600 (ttt) cc_final: 0.8341 (ttp) REVERT: A 429 ILE cc_start: 0.9015 (tp) cc_final: 0.8731 (mm) REVERT: A 445 TYR cc_start: 0.8108 (t80) cc_final: 0.7805 (t80) REVERT: B 18 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.9007 (mtmt) REVERT: B 55 MET cc_start: 0.9175 (mmm) cc_final: 0.8768 (mmt) REVERT: B 306 PHE cc_start: 0.8256 (t80) cc_final: 0.7951 (t80) REVERT: C 18 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8874 (ptpp) REVERT: C 49 MET cc_start: 0.8866 (tmm) cc_final: 0.8545 (tmm) REVERT: C 55 MET cc_start: 0.9368 (mmt) cc_final: 0.8654 (mmt) REVERT: C 95 ASP cc_start: 0.9213 (p0) cc_final: 0.8895 (p0) REVERT: C 141 ARG cc_start: 0.8669 (mtt90) cc_final: 0.8186 (mtm-85) REVERT: C 298 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8462 (tm-30) REVERT: D 14 GLU cc_start: 0.8812 (pt0) cc_final: 0.8597 (pp20) REVERT: D 18 LYS cc_start: 0.9192 (mtmm) cc_final: 0.8938 (mtmm) REVERT: D 79 LEU cc_start: 0.9255 (mp) cc_final: 0.8993 (mm) REVERT: D 220 TYR cc_start: 0.8569 (t80) cc_final: 0.8229 (t80) REVERT: D 223 LEU cc_start: 0.8933 (mt) cc_final: 0.8597 (pp) REVERT: D 227 MET cc_start: 0.8719 (mmt) cc_final: 0.8320 (tpp) REVERT: D 243 ASN cc_start: 0.7021 (t0) cc_final: 0.6614 (t0) REVERT: E 123 ASP cc_start: 0.9070 (p0) cc_final: 0.8760 (p0) REVERT: E 170 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7581 (mmmt) REVERT: K 1 GLN cc_start: 0.8272 (pm20) cc_final: 0.7745 (pm20) REVERT: K 425 ARG cc_start: 0.7974 (ptp90) cc_final: 0.7506 (ptp90) REVERT: K 452 LYS cc_start: 0.8388 (tptp) cc_final: 0.8090 (tptp) REVERT: K 481 TYR cc_start: 0.7681 (m-80) cc_final: 0.7169 (m-80) REVERT: L 425 ARG cc_start: 0.8993 (ptt90) cc_final: 0.8764 (ptt180) REVERT: L 426 GLN cc_start: 0.8765 (tt0) cc_final: 0.8558 (tp-100) REVERT: M 3 GLN cc_start: 0.8660 (mp10) cc_final: 0.8376 (pm20) REVERT: M 430 LYS cc_start: 0.8591 (tptm) cc_final: 0.8349 (mtpt) REVERT: M 452 LYS cc_start: 0.9091 (mtpt) cc_final: 0.8748 (mttm) REVERT: M 469 GLU cc_start: 0.8279 (mp0) cc_final: 0.7926 (mp0) REVERT: M 474 LYS cc_start: 0.9041 (mttt) cc_final: 0.8766 (mmtp) REVERT: M 482 TYR cc_start: 0.8600 (m-80) cc_final: 0.8349 (m-80) outliers start: 51 outliers final: 35 residues processed: 375 average time/residue: 0.1332 time to fit residues: 76.6547 Evaluate side-chains 370 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 332 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 509 THR Chi-restraints excluded: chain L residue 449 ASP Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 504 GLN Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 445 THR Chi-restraints excluded: chain M residue 467 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 62 optimal weight: 1.9990 chunk 168 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 131 optimal weight: 8.9990 chunk 96 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 76 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN C 303 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 507 GLN L 504 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.092315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.063895 restraints weight = 235870.355| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 7.60 r_work: 0.2695 rms_B_bonded: 6.42 restraints_weight: 2.0000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17328 Z= 0.197 Angle : 0.642 11.342 23680 Z= 0.323 Chirality : 0.046 0.226 2691 Planarity : 0.003 0.031 2900 Dihedral : 7.874 67.752 2920 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.26 % Allowed : 14.71 % Favored : 82.03 % 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: 1.61 (0.19), residues: 2024 helix: 1.99 (0.21), residues: 585 sheet: 1.01 (0.21), residues: 596 loop : 0.59 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 141 TYR 0.025 0.002 TYR A 277 PHE 0.023 0.002 PHE A 289 TRP 0.021 0.001 TRP A 237 HIS 0.004 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00446 (17291) covalent geometry : angle 0.63531 (23577) SS BOND : bond 0.00123 ( 8) SS BOND : angle 0.36907 ( 16) hydrogen bonds : bond 0.04057 ( 826) hydrogen bonds : angle 4.66479 ( 2623) link_ALPHA1-3 : bond 0.00897 ( 4) link_ALPHA1-3 : angle 2.05701 ( 12) link_ALPHA1-6 : bond 0.00765 ( 4) link_ALPHA1-6 : angle 1.80336 ( 12) link_BETA1-4 : bond 0.00309 ( 12) link_BETA1-4 : angle 1.65518 ( 36) link_NAG-ASN : bond 0.00178 ( 9) link_NAG-ASN : angle 1.22036 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 338 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6696 (mtp) cc_final: 0.5851 (mpp) REVERT: A 66 TYR cc_start: 0.8551 (m-80) cc_final: 0.8311 (m-80) REVERT: A 141 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8192 (mmt180) REVERT: A 227 MET cc_start: 0.8664 (ttt) cc_final: 0.8350 (ttp) REVERT: A 429 ILE cc_start: 0.9010 (tp) cc_final: 0.8727 (mm) REVERT: A 445 TYR cc_start: 0.8184 (t80) cc_final: 0.7930 (t80) REVERT: B 55 MET cc_start: 0.9205 (mmm) cc_final: 0.8821 (mmt) REVERT: B 306 PHE cc_start: 0.8286 (t80) cc_final: 0.7988 (t80) REVERT: C 18 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8689 (ptpp) REVERT: C 49 MET cc_start: 0.8848 (tmm) cc_final: 0.8491 (tmm) REVERT: C 55 MET cc_start: 0.9380 (mmt) cc_final: 0.8694 (mmt) REVERT: C 95 ASP cc_start: 0.9226 (p0) cc_final: 0.8887 (p0) REVERT: C 141 ARG cc_start: 0.8741 (mtt90) cc_final: 0.8227 (mtm-85) REVERT: C 226 TYR cc_start: 0.9305 (m-80) cc_final: 0.8851 (m-80) REVERT: C 298 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8485 (tm-30) REVERT: D 14 GLU cc_start: 0.8806 (pt0) cc_final: 0.8499 (pp20) REVERT: D 18 LYS cc_start: 0.9199 (mtmm) cc_final: 0.8775 (mtmm) REVERT: D 79 LEU cc_start: 0.9279 (mp) cc_final: 0.9030 (mm) REVERT: D 155 GLU cc_start: 0.9237 (tt0) cc_final: 0.8993 (tt0) REVERT: D 165 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8013 (pt0) REVERT: D 182 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8172 (mm-30) REVERT: D 220 TYR cc_start: 0.8589 (t80) cc_final: 0.8220 (t80) REVERT: D 223 LEU cc_start: 0.8919 (mt) cc_final: 0.8614 (pp) REVERT: D 227 MET cc_start: 0.8667 (mmt) cc_final: 0.8313 (mmm) REVERT: D 243 ASN cc_start: 0.6943 (t0) cc_final: 0.6468 (t0) REVERT: E 123 ASP cc_start: 0.9147 (p0) cc_final: 0.8863 (p0) REVERT: E 140 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8364 (mm-30) REVERT: E 170 LYS cc_start: 0.8262 (mttt) cc_final: 0.7608 (mmmt) REVERT: K 1 GLN cc_start: 0.8386 (pm20) cc_final: 0.7961 (pm20) REVERT: L 504 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7974 (pm20) REVERT: M 3 GLN cc_start: 0.8685 (mp10) cc_final: 0.8357 (mp10) REVERT: M 430 LYS cc_start: 0.8609 (tptm) cc_final: 0.8380 (mtpt) REVERT: M 452 LYS cc_start: 0.9079 (mtpt) cc_final: 0.8784 (mttm) REVERT: M 460 ASP cc_start: 0.5952 (p0) cc_final: 0.4539 (p0) REVERT: M 469 GLU cc_start: 0.8232 (mp0) cc_final: 0.7835 (mp0) REVERT: M 482 TYR cc_start: 0.8647 (m-80) cc_final: 0.8377 (m-80) outliers start: 56 outliers final: 44 residues processed: 366 average time/residue: 0.1253 time to fit residues: 70.2014 Evaluate side-chains 373 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 326 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 456 THR Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 509 THR Chi-restraints excluded: chain L residue 449 ASP Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 474 LYS Chi-restraints excluded: chain L residue 504 GLN Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 445 THR Chi-restraints excluded: chain M residue 464 ASN Chi-restraints excluded: chain M residue 467 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.092414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.063547 restraints weight = 259191.886| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 7.51 r_work: 0.2699 rms_B_bonded: 6.42 restraints_weight: 2.0000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17328 Z= 0.166 Angle : 0.633 11.763 23680 Z= 0.315 Chirality : 0.045 0.232 2691 Planarity : 0.003 0.032 2900 Dihedral : 7.571 64.992 2920 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.09 % Allowed : 15.33 % Favored : 81.58 % 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: 2024 helix: 1.93 (0.21), residues: 585 sheet: 1.15 (0.22), residues: 562 loop : 0.43 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 141 TYR 0.024 0.002 TYR A 299 PHE 0.023 0.002 PHE A 289 TRP 0.024 0.001 TRP A 237 HIS 0.003 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00376 (17291) covalent geometry : angle 0.62673 (23577) SS BOND : bond 0.00088 ( 8) SS BOND : angle 0.32705 ( 16) hydrogen bonds : bond 0.03933 ( 826) hydrogen bonds : angle 4.59686 ( 2623) link_ALPHA1-3 : bond 0.00924 ( 4) link_ALPHA1-3 : angle 2.00827 ( 12) link_ALPHA1-6 : bond 0.00815 ( 4) link_ALPHA1-6 : angle 1.73584 ( 12) link_BETA1-4 : bond 0.00304 ( 12) link_BETA1-4 : angle 1.58609 ( 36) link_NAG-ASN : bond 0.00134 ( 9) link_NAG-ASN : angle 1.18773 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 336 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6677 (mtp) cc_final: 0.5835 (mpp) REVERT: A 66 TYR cc_start: 0.8568 (m-80) cc_final: 0.8342 (m-80) REVERT: A 227 MET cc_start: 0.8664 (ttt) cc_final: 0.8357 (ttp) REVERT: A 429 ILE cc_start: 0.9022 (tp) cc_final: 0.8732 (mm) REVERT: A 445 TYR cc_start: 0.8166 (t80) cc_final: 0.7879 (t80) REVERT: B 55 MET cc_start: 0.9229 (mmm) cc_final: 0.8876 (mmt) REVERT: B 306 PHE cc_start: 0.8265 (t80) cc_final: 0.7944 (t80) REVERT: C 18 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8730 (ptpp) REVERT: C 49 MET cc_start: 0.8876 (tmm) cc_final: 0.8670 (tmm) REVERT: C 55 MET cc_start: 0.9399 (mmt) cc_final: 0.8680 (mmt) REVERT: C 95 ASP cc_start: 0.9228 (p0) cc_final: 0.8911 (p0) REVERT: C 141 ARG cc_start: 0.8756 (mtt90) cc_final: 0.8348 (mtp180) REVERT: C 298 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8467 (tm-30) REVERT: D 13 LYS cc_start: 0.9148 (tttt) cc_final: 0.8810 (tptm) REVERT: D 14 GLU cc_start: 0.8799 (pt0) cc_final: 0.8507 (pp20) REVERT: D 18 LYS cc_start: 0.9200 (mtmm) cc_final: 0.8737 (mtmm) REVERT: D 79 LEU cc_start: 0.9288 (mp) cc_final: 0.9047 (mm) REVERT: D 155 GLU cc_start: 0.9216 (tt0) cc_final: 0.8983 (tt0) REVERT: D 165 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8253 (mp0) REVERT: D 182 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8214 (mm-30) REVERT: D 220 TYR cc_start: 0.8550 (t80) cc_final: 0.8209 (t80) REVERT: D 223 LEU cc_start: 0.8912 (mt) cc_final: 0.8610 (pp) REVERT: D 227 MET cc_start: 0.8666 (mmt) cc_final: 0.8287 (mmm) REVERT: E 123 ASP cc_start: 0.9145 (p0) cc_final: 0.8854 (p0) REVERT: E 134 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: E 140 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8369 (mm-30) REVERT: E 170 LYS cc_start: 0.8270 (mttt) cc_final: 0.7636 (mmmt) REVERT: K 1 GLN cc_start: 0.8433 (pm20) cc_final: 0.8028 (pm20) REVERT: L 504 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7900 (pm20) REVERT: M 3 GLN cc_start: 0.8696 (mp10) cc_final: 0.8422 (mp10) REVERT: M 431 GLU cc_start: 0.8459 (tp30) cc_final: 0.7911 (pm20) REVERT: M 469 GLU cc_start: 0.8224 (mp0) cc_final: 0.7807 (mp0) REVERT: M 482 TYR cc_start: 0.8704 (m-80) cc_final: 0.8416 (m-80) outliers start: 53 outliers final: 40 residues processed: 362 average time/residue: 0.1236 time to fit residues: 69.1133 Evaluate side-chains 367 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 324 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 134 PHE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain L residue 449 ASP Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 474 LYS Chi-restraints excluded: chain L residue 504 GLN Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 464 ASN Chi-restraints excluded: chain M residue 467 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 44 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 179 optimal weight: 0.8980 chunk 30 optimal weight: 20.0000 chunk 119 optimal weight: 0.0870 chunk 169 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 176 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN E 200 GLN L 464 ASN L 504 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.093123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.064578 restraints weight = 228571.323| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 7.12 r_work: 0.2727 rms_B_bonded: 6.23 restraints_weight: 2.0000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 17328 Z= 0.129 Angle : 0.628 11.911 23680 Z= 0.311 Chirality : 0.045 0.234 2691 Planarity : 0.003 0.032 2900 Dihedral : 7.197 61.355 2920 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.86 % Allowed : 15.55 % Favored : 81.58 % 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: 2024 helix: 1.90 (0.21), residues: 585 sheet: 1.04 (0.22), residues: 589 loop : 0.50 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 196 TYR 0.023 0.001 TYR A 299 PHE 0.026 0.001 PHE B 301 TRP 0.025 0.001 TRP A 237 HIS 0.003 0.000 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00292 (17291) covalent geometry : angle 0.62305 (23577) SS BOND : bond 0.00115 ( 8) SS BOND : angle 0.20813 ( 16) hydrogen bonds : bond 0.03807 ( 826) hydrogen bonds : angle 4.50839 ( 2623) link_ALPHA1-3 : bond 0.00972 ( 4) link_ALPHA1-3 : angle 1.92708 ( 12) link_ALPHA1-6 : bond 0.00892 ( 4) link_ALPHA1-6 : angle 1.64968 ( 12) link_BETA1-4 : bond 0.00332 ( 12) link_BETA1-4 : angle 1.45893 ( 36) link_NAG-ASN : bond 0.00132 ( 9) link_NAG-ASN : angle 1.13334 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 338 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6660 (mtp) cc_final: 0.5856 (mpp) REVERT: A 66 TYR cc_start: 0.8560 (m-80) cc_final: 0.8343 (m-80) REVERT: A 429 ILE cc_start: 0.9004 (tp) cc_final: 0.8713 (mm) REVERT: A 445 TYR cc_start: 0.8190 (t80) cc_final: 0.7937 (t80) REVERT: B 55 MET cc_start: 0.9216 (mmm) cc_final: 0.8885 (mmt) REVERT: B 306 PHE cc_start: 0.8259 (t80) cc_final: 0.7984 (t80) REVERT: B 437 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8655 (mp) REVERT: C 18 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8829 (pttm) REVERT: C 49 MET cc_start: 0.8859 (tmm) cc_final: 0.8639 (tmm) REVERT: C 55 MET cc_start: 0.9377 (mmt) cc_final: 0.8641 (mmt) REVERT: C 68 ARG cc_start: 0.8948 (ttt180) cc_final: 0.8473 (ttm-80) REVERT: C 95 ASP cc_start: 0.9208 (p0) cc_final: 0.8925 (p0) REVERT: C 141 ARG cc_start: 0.8754 (mtt90) cc_final: 0.8346 (mtp180) REVERT: C 226 TYR cc_start: 0.9290 (m-80) cc_final: 0.9045 (m-80) REVERT: C 227 MET cc_start: 0.8907 (tpp) cc_final: 0.8653 (tpp) REVERT: C 286 MET cc_start: 0.8568 (mmm) cc_final: 0.8266 (ttp) REVERT: C 298 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8539 (tm-30) REVERT: D 13 LYS cc_start: 0.9137 (tttt) cc_final: 0.8818 (tptm) REVERT: D 14 GLU cc_start: 0.8768 (pt0) cc_final: 0.8447 (pp20) REVERT: D 18 LYS cc_start: 0.9204 (mtmm) cc_final: 0.8710 (mtmm) REVERT: D 79 LEU cc_start: 0.9279 (mp) cc_final: 0.9047 (mm) REVERT: D 165 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8183 (mp0) REVERT: D 182 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8164 (mm-30) REVERT: D 220 TYR cc_start: 0.8543 (t80) cc_final: 0.8136 (t80) REVERT: D 223 LEU cc_start: 0.8922 (mt) cc_final: 0.8606 (pp) REVERT: D 227 MET cc_start: 0.8617 (mmt) cc_final: 0.8231 (mmm) REVERT: D 243 ASN cc_start: 0.6996 (t0) cc_final: 0.6561 (t0) REVERT: E 82 ASN cc_start: 0.9149 (m-40) cc_final: 0.8598 (t0) REVERT: E 123 ASP cc_start: 0.9140 (p0) cc_final: 0.8864 (p0) REVERT: E 134 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.7693 (m-80) REVERT: E 140 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8366 (mm-30) REVERT: E 170 LYS cc_start: 0.8215 (mttt) cc_final: 0.7586 (mmmt) REVERT: K 1 GLN cc_start: 0.8433 (pm20) cc_final: 0.8007 (pm20) REVERT: L 6 GLU cc_start: 0.8508 (pm20) cc_final: 0.8083 (pm20) REVERT: L 504 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7945 (pm20) REVERT: M 3 GLN cc_start: 0.8701 (mp10) cc_final: 0.8480 (mp10) REVERT: M 4 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8534 (mt) REVERT: M 430 LYS cc_start: 0.8938 (mtpt) cc_final: 0.8574 (tptm) REVERT: M 431 GLU cc_start: 0.8327 (tp30) cc_final: 0.7927 (tm-30) REVERT: M 452 LYS cc_start: 0.9049 (mtpt) cc_final: 0.8641 (mttm) REVERT: M 469 GLU cc_start: 0.8173 (mp0) cc_final: 0.7739 (mp0) REVERT: M 482 TYR cc_start: 0.8637 (m-80) cc_final: 0.8355 (m-80) outliers start: 49 outliers final: 37 residues processed: 359 average time/residue: 0.1271 time to fit residues: 70.4767 Evaluate side-chains 365 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 323 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 134 PHE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 509 THR Chi-restraints excluded: chain L residue 449 ASP Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 474 LYS Chi-restraints excluded: chain L residue 504 GLN Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 464 ASN Chi-restraints excluded: chain M residue 465 THR Chi-restraints excluded: chain M residue 467 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 133 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 113 optimal weight: 0.0270 chunk 91 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 140 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 overall best weight: 1.7044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 426 GLN L 504 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.092847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.064205 restraints weight = 223806.209| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 7.05 r_work: 0.2724 rms_B_bonded: 6.13 restraints_weight: 2.0000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17328 Z= 0.150 Angle : 0.645 12.089 23680 Z= 0.318 Chirality : 0.045 0.238 2691 Planarity : 0.003 0.031 2900 Dihedral : 7.003 59.594 2920 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.58 % Allowed : 16.28 % Favored : 81.13 % 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: 1.50 (0.19), residues: 2024 helix: 1.85 (0.21), residues: 585 sheet: 1.13 (0.22), residues: 562 loop : 0.42 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 196 TYR 0.023 0.001 TYR A 299 PHE 0.026 0.001 PHE A 289 TRP 0.026 0.001 TRP A 237 HIS 0.003 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00342 (17291) covalent geometry : angle 0.63937 (23577) SS BOND : bond 0.00088 ( 8) SS BOND : angle 0.27654 ( 16) hydrogen bonds : bond 0.03754 ( 826) hydrogen bonds : angle 4.49623 ( 2623) link_ALPHA1-3 : bond 0.00929 ( 4) link_ALPHA1-3 : angle 1.97415 ( 12) link_ALPHA1-6 : bond 0.00904 ( 4) link_ALPHA1-6 : angle 1.65989 ( 12) link_BETA1-4 : bond 0.00338 ( 12) link_BETA1-4 : angle 1.49966 ( 36) link_NAG-ASN : bond 0.00128 ( 9) link_NAG-ASN : angle 1.17180 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 338 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6696 (mtp) cc_final: 0.5895 (mpp) REVERT: A 429 ILE cc_start: 0.9010 (tp) cc_final: 0.8710 (mm) REVERT: A 445 TYR cc_start: 0.8154 (t80) cc_final: 0.7924 (t80) REVERT: B 55 MET cc_start: 0.9212 (mmm) cc_final: 0.8882 (mmt) REVERT: B 298 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8359 (tm-30) REVERT: B 306 PHE cc_start: 0.8221 (t80) cc_final: 0.7994 (t80) REVERT: B 437 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8677 (mp) REVERT: C 18 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8854 (pttm) REVERT: C 49 MET cc_start: 0.8854 (tmm) cc_final: 0.8625 (tmm) REVERT: C 55 MET cc_start: 0.9375 (mmt) cc_final: 0.8614 (mmt) REVERT: C 95 ASP cc_start: 0.9201 (p0) cc_final: 0.8910 (p0) REVERT: C 141 ARG cc_start: 0.8780 (mtt90) cc_final: 0.8386 (mtp180) REVERT: C 226 TYR cc_start: 0.9287 (m-80) cc_final: 0.9051 (m-80) REVERT: C 227 MET cc_start: 0.8915 (tpp) cc_final: 0.8657 (tpp) REVERT: C 298 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8508 (tm-30) REVERT: D 13 LYS cc_start: 0.9141 (tttt) cc_final: 0.8780 (tptm) REVERT: D 14 GLU cc_start: 0.8810 (pt0) cc_final: 0.8489 (pp20) REVERT: D 18 LYS cc_start: 0.9207 (mtmm) cc_final: 0.8719 (mtmm) REVERT: D 79 LEU cc_start: 0.9274 (mp) cc_final: 0.9045 (mm) REVERT: D 165 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8186 (mp0) REVERT: D 182 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8181 (mm-30) REVERT: D 220 TYR cc_start: 0.8509 (t80) cc_final: 0.8153 (t80) REVERT: D 223 LEU cc_start: 0.8905 (mt) cc_final: 0.8601 (pp) REVERT: D 298 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8884 (tm-30) REVERT: E 123 ASP cc_start: 0.9157 (p0) cc_final: 0.8883 (p0) REVERT: E 134 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: E 140 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8388 (mm-30) REVERT: E 170 LYS cc_start: 0.8251 (mttt) cc_final: 0.7625 (mmmt) REVERT: K 1 GLN cc_start: 0.8416 (pm20) cc_final: 0.8003 (pm20) REVERT: K 440 TRP cc_start: 0.8543 (m100) cc_final: 0.8312 (m100) REVERT: K 461 ASN cc_start: 0.8312 (m110) cc_final: 0.8100 (m-40) REVERT: L 6 GLU cc_start: 0.8442 (pm20) cc_final: 0.8165 (pm20) REVERT: L 425 ARG cc_start: 0.9099 (ptt-90) cc_final: 0.8846 (ptt-90) REVERT: L 460 ASP cc_start: 0.8253 (t0) cc_final: 0.7875 (p0) REVERT: L 504 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8126 (pm20) REVERT: M 3 GLN cc_start: 0.8704 (mp10) cc_final: 0.8478 (mp10) REVERT: M 4 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8458 (mt) REVERT: M 430 LYS cc_start: 0.8980 (mtpt) cc_final: 0.8663 (tptt) REVERT: M 452 LYS cc_start: 0.9039 (mtpt) cc_final: 0.8662 (mttm) REVERT: M 482 TYR cc_start: 0.8679 (m-80) cc_final: 0.8383 (m-80) outliers start: 44 outliers final: 35 residues processed: 360 average time/residue: 0.1254 time to fit residues: 70.0317 Evaluate side-chains 367 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 327 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 134 PHE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain L residue 449 ASP Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 474 LYS Chi-restraints excluded: chain L residue 504 GLN Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 467 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 172 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 143 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN ** E 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 464 ASN L 504 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.091775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.062971 restraints weight = 243816.914| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 7.27 r_work: 0.2700 rms_B_bonded: 6.22 restraints_weight: 2.0000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17328 Z= 0.200 Angle : 0.673 11.808 23680 Z= 0.333 Chirality : 0.046 0.242 2691 Planarity : 0.003 0.030 2900 Dihedral : 6.973 59.461 2920 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.53 % Allowed : 16.79 % Favored : 80.69 % 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: 1.46 (0.19), residues: 2024 helix: 1.81 (0.21), residues: 585 sheet: 1.17 (0.22), residues: 556 loop : 0.37 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 99 TYR 0.035 0.002 TYR A 66 PHE 0.027 0.002 PHE A 289 TRP 0.026 0.001 TRP A 237 HIS 0.009 0.001 HIS E 240 Details of bonding type rmsd covalent geometry : bond 0.00456 (17291) covalent geometry : angle 0.66711 (23577) SS BOND : bond 0.00160 ( 8) SS BOND : angle 0.34152 ( 16) hydrogen bonds : bond 0.03832 ( 826) hydrogen bonds : angle 4.59086 ( 2623) link_ALPHA1-3 : bond 0.00887 ( 4) link_ALPHA1-3 : angle 2.05855 ( 12) link_ALPHA1-6 : bond 0.00844 ( 4) link_ALPHA1-6 : angle 1.61141 ( 12) link_BETA1-4 : bond 0.00347 ( 12) link_BETA1-4 : angle 1.61874 ( 36) link_NAG-ASN : bond 0.00186 ( 9) link_NAG-ASN : angle 1.25905 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 337 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6645 (mtp) cc_final: 0.5861 (mpp) REVERT: A 429 ILE cc_start: 0.9007 (tp) cc_final: 0.8711 (mm) REVERT: B 55 MET cc_start: 0.9225 (mmm) cc_final: 0.8698 (mmm) REVERT: B 227 MET cc_start: 0.9250 (tpp) cc_final: 0.8955 (mmm) REVERT: B 286 MET cc_start: 0.8129 (ttp) cc_final: 0.7785 (tmm) REVERT: B 298 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8392 (tm-30) REVERT: B 306 PHE cc_start: 0.8223 (t80) cc_final: 0.7995 (t80) REVERT: B 437 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8694 (mp) REVERT: C 18 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8847 (pttm) REVERT: C 49 MET cc_start: 0.8906 (tmm) cc_final: 0.8683 (tmm) REVERT: C 55 MET cc_start: 0.9383 (mmt) cc_final: 0.8631 (mmt) REVERT: C 68 ARG cc_start: 0.8976 (ttt180) cc_final: 0.8518 (ttm-80) REVERT: C 95 ASP cc_start: 0.9221 (p0) cc_final: 0.8885 (p0) REVERT: C 141 ARG cc_start: 0.8812 (mtt90) cc_final: 0.8401 (mtp180) REVERT: C 226 TYR cc_start: 0.9306 (m-80) cc_final: 0.9083 (m-80) REVERT: C 227 MET cc_start: 0.8902 (tpp) cc_final: 0.8650 (tpp) REVERT: C 298 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8454 (tm-30) REVERT: D 13 LYS cc_start: 0.9167 (tttt) cc_final: 0.8819 (tptm) REVERT: D 14 GLU cc_start: 0.8832 (pt0) cc_final: 0.8507 (pp20) REVERT: D 18 LYS cc_start: 0.9207 (mtmm) cc_final: 0.8735 (mtmm) REVERT: D 79 LEU cc_start: 0.9275 (mp) cc_final: 0.9072 (mm) REVERT: D 165 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8274 (mp0) REVERT: D 182 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8202 (mm-30) REVERT: D 220 TYR cc_start: 0.8588 (t80) cc_final: 0.8077 (t80) REVERT: D 223 LEU cc_start: 0.8902 (mt) cc_final: 0.8498 (pp) REVERT: D 227 MET cc_start: 0.8599 (mmt) cc_final: 0.8273 (mmm) REVERT: D 298 GLU cc_start: 0.9167 (tm-30) cc_final: 0.8906 (tm-30) REVERT: E 123 ASP cc_start: 0.9156 (p0) cc_final: 0.8882 (p0) REVERT: E 134 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: E 140 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8416 (mm-30) REVERT: E 170 LYS cc_start: 0.8265 (mttt) cc_final: 0.7649 (mmmt) REVERT: K 1 GLN cc_start: 0.8466 (pm20) cc_final: 0.8076 (pm20) REVERT: K 440 TRP cc_start: 0.8578 (m100) cc_final: 0.8317 (m100) REVERT: K 469 GLU cc_start: 0.7616 (mp0) cc_final: 0.7374 (mp0) REVERT: L 425 ARG cc_start: 0.9096 (ptt-90) cc_final: 0.8868 (ptt-90) REVERT: L 433 GLU cc_start: 0.9080 (tp30) cc_final: 0.8878 (tp30) REVERT: L 460 ASP cc_start: 0.8085 (t0) cc_final: 0.7661 (p0) REVERT: M 3 GLN cc_start: 0.8697 (mp10) cc_final: 0.8469 (mp10) REVERT: M 4 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8495 (mt) REVERT: M 421 MET cc_start: 0.9206 (mmm) cc_final: 0.8529 (mmm) REVERT: M 430 LYS cc_start: 0.9019 (mtpt) cc_final: 0.8645 (tptp) REVERT: M 452 LYS cc_start: 0.9066 (mtpt) cc_final: 0.8644 (mttm) REVERT: M 469 GLU cc_start: 0.7825 (mp0) cc_final: 0.7621 (mp0) REVERT: M 482 TYR cc_start: 0.8699 (m-80) cc_final: 0.8390 (m-80) outliers start: 43 outliers final: 37 residues processed: 358 average time/residue: 0.1280 time to fit residues: 70.4801 Evaluate side-chains 367 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 326 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 134 PHE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain L residue 449 ASP Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 474 LYS Chi-restraints excluded: chain L residue 504 GLN Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 445 THR Chi-restraints excluded: chain M residue 464 ASN Chi-restraints excluded: chain M residue 467 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 73 optimal weight: 0.1980 chunk 84 optimal weight: 7.9990 chunk 189 optimal weight: 0.0020 chunk 193 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 57 optimal weight: 0.5980 chunk 153 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN L 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.093441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.064938 restraints weight = 224339.366| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 7.15 r_work: 0.2741 rms_B_bonded: 6.31 restraints_weight: 2.0000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17328 Z= 0.123 Angle : 0.660 12.064 23680 Z= 0.325 Chirality : 0.045 0.235 2691 Planarity : 0.003 0.031 2900 Dihedral : 6.599 54.816 2920 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.85 % Allowed : 17.69 % Favored : 80.46 % 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: 1.40 (0.19), residues: 2024 helix: 1.68 (0.21), residues: 585 sheet: 1.12 (0.22), residues: 563 loop : 0.39 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 196 TYR 0.032 0.001 TYR A 66 PHE 0.035 0.001 PHE A 289 TRP 0.044 0.001 TRP A 237 HIS 0.003 0.000 HIS E 240 Details of bonding type rmsd covalent geometry : bond 0.00276 (17291) covalent geometry : angle 0.65549 (23577) SS BOND : bond 0.00190 ( 8) SS BOND : angle 0.33250 ( 16) hydrogen bonds : bond 0.03737 ( 826) hydrogen bonds : angle 4.51163 ( 2623) link_ALPHA1-3 : bond 0.01014 ( 4) link_ALPHA1-3 : angle 1.85505 ( 12) link_ALPHA1-6 : bond 0.00993 ( 4) link_ALPHA1-6 : angle 1.49358 ( 12) link_BETA1-4 : bond 0.00376 ( 12) link_BETA1-4 : angle 1.40054 ( 36) link_NAG-ASN : bond 0.00152 ( 9) link_NAG-ASN : angle 1.10155 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 344 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6639 (mtp) cc_final: 0.5881 (mpp) REVERT: A 429 ILE cc_start: 0.9015 (tp) cc_final: 0.8717 (mm) REVERT: B 55 MET cc_start: 0.9199 (mmm) cc_final: 0.8927 (mmt) REVERT: B 227 MET cc_start: 0.9220 (tpp) cc_final: 0.8980 (mmm) REVERT: B 286 MET cc_start: 0.8064 (ttp) cc_final: 0.7736 (ppp) REVERT: B 298 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8312 (tm-30) REVERT: B 306 PHE cc_start: 0.8200 (t80) cc_final: 0.7986 (t80) REVERT: B 437 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8712 (mp) REVERT: C 18 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8861 (pttm) REVERT: C 49 MET cc_start: 0.8911 (tmm) cc_final: 0.8685 (tmm) REVERT: C 55 MET cc_start: 0.9384 (mmt) cc_final: 0.8619 (mmt) REVERT: C 68 ARG cc_start: 0.8959 (ttt180) cc_final: 0.8522 (ttm-80) REVERT: C 95 ASP cc_start: 0.9182 (p0) cc_final: 0.8928 (p0) REVERT: C 141 ARG cc_start: 0.8762 (mtt90) cc_final: 0.8396 (mtp180) REVERT: C 298 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8392 (tm-30) REVERT: D 13 LYS cc_start: 0.9163 (tttt) cc_final: 0.8821 (tptm) REVERT: D 14 GLU cc_start: 0.8839 (pt0) cc_final: 0.8507 (pp20) REVERT: D 18 LYS cc_start: 0.9199 (mtmm) cc_final: 0.8749 (mtmm) REVERT: D 52 GLU cc_start: 0.8841 (mp0) cc_final: 0.8481 (mp0) REVERT: D 79 LEU cc_start: 0.9277 (mp) cc_final: 0.9048 (mm) REVERT: D 165 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8180 (mp0) REVERT: D 182 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8235 (mm-30) REVERT: D 227 MET cc_start: 0.8591 (mmt) cc_final: 0.8266 (mmm) REVERT: D 243 ASN cc_start: 0.7008 (t0) cc_final: 0.6576 (t0) REVERT: D 298 GLU cc_start: 0.9158 (tm-30) cc_final: 0.8880 (tm-30) REVERT: E 82 ASN cc_start: 0.9159 (m-40) cc_final: 0.8629 (t0) REVERT: E 123 ASP cc_start: 0.9149 (p0) cc_final: 0.8867 (p0) REVERT: E 134 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.7663 (m-80) REVERT: E 140 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8385 (mm-30) REVERT: E 170 LYS cc_start: 0.8233 (mttt) cc_final: 0.7629 (mmmt) REVERT: E 179 MET cc_start: 0.8749 (mmm) cc_final: 0.8294 (mmm) REVERT: K 1 GLN cc_start: 0.8460 (pm20) cc_final: 0.8089 (pm20) REVERT: K 440 TRP cc_start: 0.8479 (m100) cc_final: 0.8278 (m100) REVERT: K 469 GLU cc_start: 0.7633 (mp0) cc_final: 0.7386 (mp0) REVERT: L 460 ASP cc_start: 0.8051 (t0) cc_final: 0.7638 (p0) REVERT: L 504 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8002 (pm20) REVERT: M 3 GLN cc_start: 0.8738 (mp10) cc_final: 0.8516 (mp10) REVERT: M 4 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8472 (mt) REVERT: M 421 MET cc_start: 0.9183 (mmm) cc_final: 0.8530 (mmm) REVERT: M 430 LYS cc_start: 0.9006 (mtpt) cc_final: 0.8632 (tptp) REVERT: M 452 LYS cc_start: 0.9009 (mtpt) cc_final: 0.8598 (mttm) REVERT: M 482 TYR cc_start: 0.8707 (m-80) cc_final: 0.8420 (m-80) outliers start: 31 outliers final: 25 residues processed: 359 average time/residue: 0.1293 time to fit residues: 71.0905 Evaluate side-chains 353 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 323 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 134 PHE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 449 ASP Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 474 LYS Chi-restraints excluded: chain L residue 504 GLN Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 467 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 181 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 2 optimal weight: 0.0570 chunk 13 optimal weight: 0.1980 chunk 159 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN E 240 HIS L 504 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.092478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.063969 restraints weight = 231385.631| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 7.16 r_work: 0.2714 rms_B_bonded: 6.25 restraints_weight: 2.0000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17328 Z= 0.159 Angle : 0.678 15.102 23680 Z= 0.334 Chirality : 0.046 0.239 2691 Planarity : 0.004 0.083 2900 Dihedral : 6.516 53.927 2920 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.02 % Allowed : 18.02 % Favored : 79.96 % 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: 1.36 (0.19), residues: 2024 helix: 1.67 (0.21), residues: 585 sheet: 1.11 (0.22), residues: 563 loop : 0.34 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 298 TYR 0.028 0.002 TYR C 220 PHE 0.032 0.002 PHE A 289 TRP 0.041 0.001 TRP A 237 HIS 0.004 0.001 HIS E 240 Details of bonding type rmsd covalent geometry : bond 0.00369 (17291) covalent geometry : angle 0.67288 (23577) SS BOND : bond 0.00177 ( 8) SS BOND : angle 0.30390 ( 16) hydrogen bonds : bond 0.03801 ( 826) hydrogen bonds : angle 4.57336 ( 2623) link_ALPHA1-3 : bond 0.00949 ( 4) link_ALPHA1-3 : angle 1.99222 ( 12) link_ALPHA1-6 : bond 0.00958 ( 4) link_ALPHA1-6 : angle 1.54731 ( 12) link_BETA1-4 : bond 0.00368 ( 12) link_BETA1-4 : angle 1.49665 ( 36) link_NAG-ASN : bond 0.00137 ( 9) link_NAG-ASN : angle 1.18878 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5068.52 seconds wall clock time: 87 minutes 29.06 seconds (5249.06 seconds total)