Starting phenix.real_space_refine on Sat Jul 4 00:04:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qnd_14075/07_2026/7qnd_14075.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qnd_14075/07_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_14075/07_2026/7qnd_14075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qnd_14075/07_2026/7qnd_14075.map" model { file = "/net/cci-nas-00/data/ceres_data/7qnd_14075/07_2026/7qnd_14075.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qnd_14075/07_2026/7qnd_14075.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7qnd_14075/07_2026/7qnd_14075.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qnd_14075/07_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-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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: 5.73, per 1000 atoms: 0.34 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: 1.56 Conformation dependent library (CDL) restraints added in 1.0 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: 0.54 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: 3.07 Time building geometry restraints manager: 2.04 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 - 16.89: 9625 16.89 - 33.78: 240 33.78 - 50.67: 31 50.67 - 67.56: 0 67.56 - 84.45: 7 Dihedral angle restraints: 9903 sinusoidal: 3899 harmonic: 6004 Sorted by residual: dihedral pdb=" N LEU D 253 " pdb=" CA LEU D 253 " pdb=" CB LEU D 253 " pdb=" CG LEU D 253 " ideal model delta sinusoidal sigma weight residual 180.00 -135.39 -44.61 3 1.50e+01 4.44e-03 8.02e+00 dihedral pdb=" N LEU C 253 " pdb=" CA LEU C 253 " pdb=" CB LEU C 253 " pdb=" CG LEU C 253 " ideal model delta sinusoidal sigma weight residual 180.00 -135.40 -44.60 3 1.50e+01 4.44e-03 8.02e+00 dihedral pdb=" N LEU A 253 " pdb=" CA LEU A 253 " pdb=" CB LEU A 253 " pdb=" CG LEU A 253 " ideal model delta sinusoidal sigma weight residual -180.00 -135.45 -44.55 3 1.50e+01 4.44e-03 8.01e+00 ... (remaining 9900 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.180 Find NCS groups from input model: 0.290 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: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 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 : 7.871 84.449 6065 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/Z covalent geometry : bond 0.00260 / 0.13 (17291) covalent geometry : angle 0.45770 / 0.21 (23577) SS BOND : bond 0.00054 / 0.04 ( 8) SS BOND : angle 0.40503 / 0.26 ( 16) hydrogen bonds : bond 0.22291 / 14.62 ( 826) hydrogen bonds : angle 7.19371 / 5.17 ( 2623) link_ALPHA1-3 : bond 0.00114 / 0.06 ( 4) link_ALPHA1-3 : angle 0.91731 / 0.54 ( 12) link_ALPHA1-6 : bond 0.00038 / 0.02 ( 4) link_ALPHA1-6 : angle 0.90757 / 0.51 ( 12) link_BETA1-4 : bond 0.00119 / 0.07 ( 12) link_BETA1-4 : angle 1.07298 / 0.66 ( 36) link_NAG-ASN : bond 0.00122 / 0.09 ( 9) link_NAG-ASN : angle 1.07846 / 0.78 ( 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 : 0.687 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: 0.6044 (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: 0.7813 (m-80) 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: 0.7728 (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: 0.8166 (mtp180) REVERT: C 274 LYS cc_start: 0.8927 (mttt) cc_final: 0.8712 (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: 0.6724 (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: 0.7916 (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: 0.8804 (m) REVERT: E 332 HIS cc_start: 0.8807 (t70) cc_final: 0.8590 (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: 0.8367 (t) outliers start: 8 outliers final: 0 residues processed: 608 average time/residue: 0.1437 time to fit residues: 127.4867 Evaluate side-chains 377 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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: 1.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3631 r_free = 0.3631 target = 0.097235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.068756 restraints weight = 277591.475| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 8.28 r_work: 0.2805 rms_B_bonded: 6.88 restraints_weight: 2.0000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17328 Z= 0.153 Angle : 0.674 13.137 23680 Z= 0.340 Chirality : 0.045 0.219 2691 Planarity : 0.004 0.043 2900 Dihedral : 4.581 79.604 2335 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.08 % Allowed : 12.86 % Favored : 85.06 % 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: 2.27 (0.19), residues: 2024 helix: 2.47 (0.21), residues: 583 sheet: 1.32 (0.21), residues: 642 loop : 1.09 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 141 TYR 0.025 0.002 TYR D 284 PHE 0.019 0.002 PHE A 221 TRP 0.016 0.001 TRP D 237 HIS 0.004 0.001 HIS D 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (17291) covalent geometry : angle 0.67110 / 0.34 (23577) SS BOND : bond 0.00216 / 0.15 ( 8) SS BOND : angle 0.59399 / 0.37 ( 16) hydrogen bonds : bond 0.05373 / 3.52 ( 826) hydrogen bonds : angle 5.11252 / 3.67 ( 2623) link_ALPHA1-3 : bond 0.00335 / 0.21 ( 4) link_ALPHA1-3 : angle 1.41467 / 1.02 ( 12) link_ALPHA1-6 : bond 0.00491 / 0.30 ( 4) link_ALPHA1-6 : angle 1.38486 / 1.00 ( 12) link_BETA1-4 : bond 0.00284 / 0.16 ( 12) link_BETA1-4 : angle 1.31758 / 0.98 ( 36) link_NAG-ASN : bond 0.00146 / 0.10 ( 9) link_NAG-ASN : angle 1.17601 / 0.82 ( 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 441 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 404 time to evaluate : 0.651 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 66 TYR cc_start: 0.8457 (m-80) cc_final: 0.8184 (m-80) REVERT: A 89 ASP cc_start: 0.9248 (t0) cc_final: 0.8969 (p0) REVERT: A 141 ARG cc_start: 0.8505 (mtt90) cc_final: 0.8175 (mtt90) REVERT: A 429 ILE cc_start: 0.9010 (tp) cc_final: 0.8732 (mm) REVERT: B 18 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8870 (mtmt) REVERT: B 55 MET cc_start: 0.9090 (mmm) cc_final: 0.8631 (mmt) REVERT: B 90 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7914 (mp10) REVERT: B 278 VAL cc_start: 0.8799 (t) cc_final: 0.8591 (p) REVERT: B 306 PHE cc_start: 0.8412 (t80) cc_final: 0.7981 (t80) REVERT: B 425 ARG cc_start: 0.8644 (ttt180) cc_final: 0.8115 (mtt180) REVERT: C 18 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8797 (ptpp) REVERT: C 55 MET cc_start: 0.9352 (mmt) cc_final: 0.8657 (mmt) REVERT: C 141 ARG cc_start: 0.8634 (mtt90) cc_final: 0.8190 (mtm-85) REVERT: C 226 TYR cc_start: 0.9176 (m-80) cc_final: 0.8946 (m-80) REVERT: C 267 HIS cc_start: 0.8346 (m90) cc_final: 0.8124 (m90) REVERT: C 270 GLU cc_start: 0.8057 (pt0) cc_final: 0.7815 (pp20) REVERT: C 277 TYR cc_start: 0.8187 (p90) cc_final: 0.7377 (p90) REVERT: C 286 MET cc_start: 0.8565 (mmm) cc_final: 0.7908 (ttp) REVERT: D 14 GLU cc_start: 0.8855 (pt0) cc_final: 0.8626 (pp20) REVERT: D 18 LYS cc_start: 0.9101 (mtmm) cc_final: 0.8812 (mtmm) REVERT: D 55 MET cc_start: 0.9100 (mmt) cc_final: 0.8499 (mmt) REVERT: D 165 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8483 (mp0) REVERT: D 220 TYR cc_start: 0.8637 (t80) cc_final: 0.8276 (t80) REVERT: D 223 LEU cc_start: 0.8968 (mt) cc_final: 0.8547 (pp) REVERT: D 227 MET cc_start: 0.8680 (mmt) cc_final: 0.8380 (tpp) REVERT: D 243 ASN cc_start: 0.7273 (t0) cc_final: 0.6893 (t0) REVERT: D 270 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7920 (mm-30) REVERT: D 425 ARG cc_start: 0.8978 (ttt180) cc_final: 0.8704 (ttm170) REVERT: E 222 THR cc_start: 0.9058 (m) cc_final: 0.8838 (p) REVERT: E 327 GLU cc_start: 0.9209 (tm-30) cc_final: 0.8872 (tm-30) REVERT: E 332 HIS cc_start: 0.8820 (t70) cc_final: 0.8606 (t70) REVERT: K 456 THR cc_start: 0.7918 (p) cc_final: 0.7698 (p) REVERT: K 469 GLU cc_start: 0.6897 (mp0) cc_final: 0.6073 (mp0) REVERT: L 459 ARG cc_start: 0.8239 (pmt-80) cc_final: 0.7736 (ppt170) REVERT: L 474 LYS cc_start: 0.8947 (mttt) cc_final: 0.8700 (pttt) REVERT: M 3 GLN cc_start: 0.8524 (mp10) cc_final: 0.8278 (pm20) REVERT: M 452 LYS cc_start: 0.9112 (mtpt) cc_final: 0.8827 (mttm) REVERT: M 464 ASN cc_start: 0.8793 (m-40) cc_final: 0.8590 (m-40) REVERT: M 469 GLU cc_start: 0.8183 (mp0) cc_final: 0.7909 (mp0) REVERT: M 474 LYS cc_start: 0.8986 (mttt) cc_final: 0.8623 (mtmm) REVERT: M 481 TYR cc_start: 0.8338 (m-80) cc_final: 0.8123 (m-10) outliers start: 37 outliers final: 19 residues processed: 421 average time/residue: 0.1322 time to fit residues: 85.1612 Evaluate side-chains 374 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 352 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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: 5.9990 chunk 106 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 120 optimal weight: 0.1980 chunk 63 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3582 r_free = 0.3582 target = 0.094649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.065965 restraints weight = 246874.819| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 7.93 r_work: 0.2738 rms_B_bonded: 6.65 restraints_weight: 2.0000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17328 Z= 0.180 Angle : 0.629 11.158 23680 Z= 0.320 Chirality : 0.044 0.173 2691 Planarity : 0.004 0.045 2900 Dihedral : 4.370 51.886 2335 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: 1.93 (0.19), residues: 2024 helix: 2.25 (0.21), residues: 585 sheet: 1.08 (0.20), residues: 648 loop : 0.86 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 141 TYR 0.024 0.002 TYR A 445 PHE 0.021 0.002 PHE D 63 TRP 0.024 0.001 TRP D 237 HIS 0.003 0.001 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (17291) covalent geometry : angle 0.62469 / 0.32 (23577) SS BOND : bond 0.00163 / 0.11 ( 8) SS BOND : angle 0.38777 / 0.27 ( 16) hydrogen bonds : bond 0.04701 / 3.05 ( 826) hydrogen bonds : angle 4.82349 / 3.46 ( 2623) link_ALPHA1-3 : bond 0.00312 / 0.20 ( 4) link_ALPHA1-3 : angle 1.45652 / 1.07 ( 12) link_ALPHA1-6 : bond 0.00487 / 0.30 ( 4) link_ALPHA1-6 : angle 1.36240 / 1.02 ( 12) link_BETA1-4 : bond 0.00286 / 0.16 ( 12) link_BETA1-4 : angle 1.47662 / 1.06 ( 36) link_NAG-ASN : bond 0.00149 / 0.09 ( 9) link_NAG-ASN : angle 1.12580 / 0.79 ( 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 400 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 360 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: symmetry clash REVERT: A 9 MET cc_start: 0.6830 (mtp) cc_final: 0.5875 (mpp) REVERT: A 66 TYR cc_start: 0.8531 (m-80) cc_final: 0.8221 (m-80) REVERT: A 429 ILE cc_start: 0.8990 (tp) cc_final: 0.8721 (mm) REVERT: A 445 TYR cc_start: 0.8119 (t80) cc_final: 0.7898 (t80) REVERT: B 18 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8994 (mtmt) REVERT: B 55 MET cc_start: 0.9170 (mmm) cc_final: 0.8645 (mmt) REVERT: B 306 PHE cc_start: 0.8277 (t80) cc_final: 0.7981 (t80) REVERT: C 18 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8616 (ptpp) REVERT: C 52 GLU cc_start: 0.8906 (mp0) cc_final: 0.8503 (mm-30) REVERT: C 55 MET cc_start: 0.9363 (mmt) cc_final: 0.8743 (mmt) REVERT: C 95 ASP cc_start: 0.9184 (p0) cc_final: 0.8886 (p0) REVERT: C 141 ARG cc_start: 0.8673 (mtt90) cc_final: 0.8174 (mtm-85) REVERT: C 226 TYR cc_start: 0.9291 (m-80) cc_final: 0.9061 (m-80) REVERT: C 267 HIS cc_start: 0.8430 (m90) cc_final: 0.8151 (m90) REVERT: C 270 GLU cc_start: 0.8043 (pt0) cc_final: 0.7745 (pp20) REVERT: C 298 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8453 (tm-30) REVERT: D 14 GLU cc_start: 0.8839 (pt0) cc_final: 0.8634 (pp20) REVERT: D 18 LYS cc_start: 0.9167 (mtmm) cc_final: 0.8921 (mtmm) REVERT: D 220 TYR cc_start: 0.8594 (t80) cc_final: 0.8275 (t80) REVERT: D 223 LEU cc_start: 0.8892 (mt) cc_final: 0.8542 (pp) REVERT: D 227 MET cc_start: 0.8694 (mmt) cc_final: 0.8315 (tpp) REVERT: D 243 ASN cc_start: 0.7009 (t0) cc_final: 0.6801 (t0) REVERT: D 270 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7834 (mm-30) REVERT: E 83 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8562 (mmm) REVERT: E 170 LYS cc_start: 0.8190 (mttt) cc_final: 0.7551 (mmmt) REVERT: E 222 THR cc_start: 0.9056 (m) cc_final: 0.8766 (p) REVERT: E 255 TYR cc_start: 0.8104 (m-80) cc_final: 0.7835 (m-80) REVERT: E 332 HIS cc_start: 0.8832 (t70) cc_final: 0.8616 (t70) REVERT: K 1 GLN cc_start: 0.8325 (pm20) cc_final: 0.7986 (pm20) REVERT: K 504 GLN cc_start: 0.8807 (mp10) cc_final: 0.8530 (pm20) REVERT: L 459 ARG cc_start: 0.8247 (pmt-80) cc_final: 0.7566 (ppt170) REVERT: L 474 LYS cc_start: 0.8945 (mttt) cc_final: 0.8666 (pttt) REVERT: M 3 GLN cc_start: 0.8585 (mp10) cc_final: 0.8314 (pm20) REVERT: M 452 LYS cc_start: 0.9109 (mtpt) cc_final: 0.8806 (mttm) REVERT: M 469 GLU cc_start: 0.8302 (mp0) cc_final: 0.7996 (mp0) REVERT: M 474 LYS cc_start: 0.8994 (mttt) cc_final: 0.8616 (mtmm) outliers start: 40 outliers final: 30 residues processed: 380 average time/residue: 0.1336 time to fit residues: 77.6665 Evaluate side-chains 367 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 334 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 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 437 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain L residue 3 GLN 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 138 optimal weight: 0.0870 chunk 44 optimal weight: 6.9990 chunk 188 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 137 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 414 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.094356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.065781 restraints weight = 243994.991| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 7.90 r_work: 0.2733 rms_B_bonded: 6.62 restraints_weight: 2.0000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 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 = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17328 Z= 0.149 Angle : 0.614 11.555 23680 Z= 0.309 Chirality : 0.044 0.278 2691 Planarity : 0.003 0.035 2900 Dihedral : 4.230 35.032 2335 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.58 % Allowed : 14.94 % Favored : 82.48 % 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: 1.77 (0.19), residues: 2024 helix: 2.10 (0.21), residues: 585 sheet: 1.25 (0.22), residues: 562 loop : 0.61 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 114 TYR 0.023 0.002 TYR A 299 PHE 0.016 0.001 PHE D 63 TRP 0.022 0.001 TRP D 237 HIS 0.002 0.001 HIS C 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (17291) covalent geometry : angle 0.61018 / 0.31 (23577) SS BOND : bond 0.00131 / 0.09 ( 8) SS BOND : angle 0.31972 / 0.22 ( 16) hydrogen bonds : bond 0.04193 / 2.71 ( 826) hydrogen bonds : angle 4.63479 / 3.33 ( 2623) link_ALPHA1-3 : bond 0.00361 / 0.22 ( 4) link_ALPHA1-3 : angle 1.41870 / 1.04 ( 12) link_ALPHA1-6 : bond 0.00377 / 0.23 ( 4) link_ALPHA1-6 : angle 1.35829 / 1.01 ( 12) link_BETA1-4 : bond 0.00269 / 0.15 ( 12) link_BETA1-4 : angle 1.44113 / 1.02 ( 36) link_NAG-ASN : bond 0.00106 / 0.07 ( 9) link_NAG-ASN : angle 1.08034 / 0.77 ( 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 390 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 345 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6785 (mtp) cc_final: 0.5877 (mpp) REVERT: A 66 TYR cc_start: 0.8549 (m-80) cc_final: 0.8258 (m-80) REVERT: A 227 MET cc_start: 0.8688 (ttt) cc_final: 0.8421 (ttp) REVERT: A 429 ILE cc_start: 0.9006 (tp) cc_final: 0.8729 (mm) REVERT: A 445 TYR cc_start: 0.8112 (t80) cc_final: 0.7840 (t80) REVERT: B 18 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.9010 (mtmt) REVERT: B 55 MET cc_start: 0.9209 (mmm) cc_final: 0.8735 (mmt) REVERT: B 306 PHE cc_start: 0.8279 (t80) cc_final: 0.7992 (t80) REVERT: C 18 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8874 (ptpp) REVERT: C 55 MET cc_start: 0.9376 (mmt) cc_final: 0.8745 (mmt) REVERT: C 95 ASP cc_start: 0.9208 (p0) cc_final: 0.8889 (p0) REVERT: C 141 ARG cc_start: 0.8695 (mtt90) cc_final: 0.8199 (mtm-85) REVERT: C 298 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8494 (tm-30) REVERT: D 14 GLU cc_start: 0.8832 (pt0) cc_final: 0.8564 (pp20) REVERT: D 18 LYS cc_start: 0.9197 (mtmm) cc_final: 0.8820 (mtmm) REVERT: D 165 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8285 (mp0) REVERT: D 220 TYR cc_start: 0.8606 (t80) cc_final: 0.8236 (t80) REVERT: D 223 LEU cc_start: 0.8921 (mt) cc_final: 0.8585 (pp) REVERT: D 227 MET cc_start: 0.8703 (mmt) cc_final: 0.8303 (tpp) REVERT: D 243 ASN cc_start: 0.6936 (t0) cc_final: 0.6546 (t0) REVERT: E 123 ASP cc_start: 0.9096 (p0) cc_final: 0.8790 (p0) REVERT: E 170 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7513 (mmmt) REVERT: E 222 THR cc_start: 0.9031 (m) cc_final: 0.8744 (p) REVERT: E 301 LEU cc_start: 0.7779 (mt) cc_final: 0.7558 (mp) REVERT: E 332 HIS cc_start: 0.8803 (t70) cc_final: 0.8584 (t70) REVERT: K 1 GLN cc_start: 0.8276 (pm20) cc_final: 0.7749 (pm20) REVERT: K 504 GLN cc_start: 0.8897 (mp10) cc_final: 0.8652 (pm20) REVERT: L 459 ARG cc_start: 0.8316 (pmt-80) cc_final: 0.8106 (pmt-80) REVERT: L 474 LYS cc_start: 0.8969 (mttt) cc_final: 0.8717 (pttt) REVERT: M 3 GLN cc_start: 0.8683 (mp10) cc_final: 0.8397 (pm20) REVERT: M 430 LYS cc_start: 0.8605 (tptm) cc_final: 0.8345 (mtpt) REVERT: M 452 LYS cc_start: 0.9099 (mtpt) cc_final: 0.8815 (mttm) REVERT: M 460 ASP cc_start: 0.5858 (p0) cc_final: 0.4510 (p0) REVERT: M 469 GLU cc_start: 0.8314 (mp0) cc_final: 0.7971 (mp0) REVERT: M 472 ASN cc_start: 0.9151 (t0) cc_final: 0.8911 (t0) REVERT: M 482 TYR cc_start: 0.8601 (m-80) cc_final: 0.8348 (m-80) outliers start: 45 outliers final: 30 residues processed: 371 average time/residue: 0.1214 time to fit residues: 68.7663 Evaluate side-chains 366 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 333 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 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 437 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 198 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 103 LYS 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 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 L residue 3 GLN 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 493 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 62 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 131 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 303 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 = 0.3521 r_free = 0.3521 target = 0.091060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.062356 restraints weight = 234532.145| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 7.12 r_work: 0.2676 rms_B_bonded: 6.21 restraints_weight: 2.0000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.2683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17328 Z= 0.235 Angle : 0.667 10.764 23680 Z= 0.339 Chirality : 0.045 0.163 2691 Planarity : 0.004 0.076 2900 Dihedral : 4.451 25.375 2335 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.43 % Allowed : 14.54 % 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: 1.51 (0.19), residues: 2024 helix: 1.90 (0.21), residues: 585 sheet: 0.97 (0.21), residues: 595 loop : 0.52 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 141 TYR 0.027 0.002 TYR A 277 PHE 0.020 0.002 PHE C 307 TRP 0.031 0.002 TRP D 237 HIS 0.005 0.001 HIS C 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.24 (17291) covalent geometry : angle 0.66156 / 0.34 (23577) SS BOND : bond 0.00150 / 0.10 ( 8) SS BOND : angle 0.43269 / 0.31 ( 16) hydrogen bonds : bond 0.04224 / 2.77 ( 826) hydrogen bonds : angle 4.71239 / 3.38 ( 2623) link_ALPHA1-3 : bond 0.00230 / 0.15 ( 4) link_ALPHA1-3 : angle 1.54965 / 1.15 ( 12) link_ALPHA1-6 : bond 0.00304 / 0.19 ( 4) link_ALPHA1-6 : angle 1.38395 / 1.08 ( 12) link_BETA1-4 : bond 0.00337 / 0.19 ( 12) link_BETA1-4 : angle 1.79402 / 1.25 ( 36) link_NAG-ASN : bond 0.00269 / 0.18 ( 9) link_NAG-ASN : angle 1.33619 / 0.96 ( 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 396 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 337 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6607 (mtp) cc_final: 0.5790 (mpp) REVERT: A 66 TYR cc_start: 0.8565 (m-80) cc_final: 0.8326 (m-80) REVERT: A 141 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8338 (mmt180) REVERT: A 227 MET cc_start: 0.8729 (ttt) cc_final: 0.8505 (ttp) REVERT: A 429 ILE cc_start: 0.9029 (tp) cc_final: 0.8735 (mm) REVERT: A 445 TYR cc_start: 0.8192 (t80) cc_final: 0.7926 (t80) REVERT: B 55 MET cc_start: 0.9281 (mmm) cc_final: 0.8958 (mmt) REVERT: B 306 PHE cc_start: 0.8247 (t80) cc_final: 0.7954 (t80) REVERT: C 18 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8902 (ptpp) REVERT: C 55 MET cc_start: 0.9393 (mmt) cc_final: 0.8752 (mmt) REVERT: C 68 ARG cc_start: 0.8994 (ttt180) cc_final: 0.8515 (ttm-80) REVERT: C 95 ASP cc_start: 0.9216 (p0) cc_final: 0.8871 (p0) REVERT: C 141 ARG cc_start: 0.8813 (mtt90) cc_final: 0.8410 (mtp180) REVERT: C 226 TYR cc_start: 0.9306 (m-80) cc_final: 0.8958 (m-80) REVERT: C 277 TYR cc_start: 0.8386 (p90) cc_final: 0.7586 (p90) REVERT: C 298 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8496 (tm-30) REVERT: D 14 GLU cc_start: 0.8842 (pt0) cc_final: 0.8548 (pp20) REVERT: D 18 LYS cc_start: 0.9213 (mtmm) cc_final: 0.8805 (mtmm) REVERT: D 165 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8274 (mp0) REVERT: D 180 ARG cc_start: 0.7707 (mmp80) cc_final: 0.7363 (mmp80) REVERT: D 182 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8206 (mm-30) REVERT: D 223 LEU cc_start: 0.8930 (mt) cc_final: 0.8602 (pp) REVERT: D 243 ASN cc_start: 0.6935 (t0) cc_final: 0.6464 (t0) REVERT: E 123 ASP cc_start: 0.9189 (p0) cc_final: 0.8905 (p0) REVERT: E 140 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8383 (mm-30) REVERT: E 170 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7657 (mmmt) REVERT: E 333 PHE cc_start: 0.8496 (t80) cc_final: 0.7840 (t80) REVERT: K 1 GLN cc_start: 0.8415 (pm20) cc_final: 0.8001 (pm20) REVERT: K 482 TYR cc_start: 0.8424 (m-10) cc_final: 0.8166 (m-10) REVERT: M 3 GLN cc_start: 0.8702 (mp10) cc_final: 0.8383 (mp10) REVERT: M 421 MET cc_start: 0.9230 (mmm) cc_final: 0.8596 (mmm) REVERT: M 431 GLU cc_start: 0.8437 (tp30) cc_final: 0.7879 (pm20) REVERT: M 452 LYS cc_start: 0.9076 (mtpt) cc_final: 0.8732 (mttm) REVERT: M 469 GLU cc_start: 0.8252 (mp0) cc_final: 0.7852 (mp0) REVERT: M 482 TYR cc_start: 0.8743 (m-80) cc_final: 0.8467 (m-80) outliers start: 59 outliers final: 42 residues processed: 368 average time/residue: 0.1309 time to fit residues: 74.0071 Evaluate side-chains 363 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 318 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 141 ARG Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 437 LEU 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 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 115 MET Chi-restraints excluded: chain C residue 198 VAL 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 145 LEU Chi-restraints excluded: chain D residue 238 VAL 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 170 LYS Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain K residue 2 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 3 GLN 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 L residue 509 THR 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: 4.9990 chunk 15 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 19 optimal weight: 0.1980 chunk 138 optimal weight: 5.9990 chunk 190 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 414 HIS L 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.092226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.063538 restraints weight = 260501.725| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 7.92 r_work: 0.2682 rms_B_bonded: 6.62 restraints_weight: 2.0000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17328 Z= 0.151 Angle : 0.624 11.690 23680 Z= 0.313 Chirality : 0.044 0.189 2691 Planarity : 0.003 0.033 2900 Dihedral : 4.292 23.276 2335 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.75 % Allowed : 15.78 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.19), residues: 2024 helix: 1.93 (0.21), residues: 585 sheet: 1.09 (0.22), residues: 562 loop : 0.37 (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 0.025 0.001 TRP D 237 HIS 0.002 0.001 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (17291) covalent geometry : angle 0.61966 / 0.31 (23577) SS BOND : bond 0.00090 / 0.06 ( 8) SS BOND : angle 0.27289 / 0.19 ( 16) hydrogen bonds : bond 0.03958 / 2.57 ( 826) hydrogen bonds : angle 4.59138 / 3.29 ( 2623) link_ALPHA1-3 : bond 0.00321 / 0.20 ( 4) link_ALPHA1-3 : angle 1.45755 / 1.07 ( 12) link_ALPHA1-6 : bond 0.00301 / 0.19 ( 4) link_ALPHA1-6 : angle 1.42874 / 1.08 ( 12) link_BETA1-4 : bond 0.00259 / 0.15 ( 12) link_BETA1-4 : angle 1.57078 / 1.11 ( 36) link_NAG-ASN : bond 0.00132 / 0.08 ( 9) link_NAG-ASN : angle 1.14909 / 0.84 ( 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 392 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 345 time to evaluate : 0.674 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: 0.6669 (mtp) cc_final: 0.5821 (mpp) REVERT: A 66 TYR cc_start: 0.8629 (m-80) cc_final: 0.8406 (m-80) REVERT: A 227 MET cc_start: 0.8698 (ttt) cc_final: 0.8401 (ttp) REVERT: A 286 MET cc_start: 0.8863 (mmm) cc_final: 0.8565 (mmm) REVERT: A 429 ILE cc_start: 0.9006 (tp) cc_final: 0.8718 (mm) REVERT: A 445 TYR cc_start: 0.8226 (t80) cc_final: 0.7959 (t80) REVERT: B 18 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.9011 (mtmt) REVERT: B 55 MET cc_start: 0.9224 (mmm) cc_final: 0.8884 (mmt) REVERT: B 306 PHE cc_start: 0.8255 (t80) cc_final: 0.7940 (t80) REVERT: C 18 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8737 (ptpp) REVERT: C 55 MET cc_start: 0.9404 (mmt) cc_final: 0.8669 (mmt) REVERT: C 68 ARG cc_start: 0.8986 (ttt180) cc_final: 0.8512 (ttm-80) REVERT: C 95 ASP cc_start: 0.9246 (p0) cc_final: 0.8960 (p0) REVERT: C 141 ARG cc_start: 0.8810 (mtt90) cc_final: 0.8408 (mtp180) REVERT: C 226 TYR cc_start: 0.9316 (m-80) cc_final: 0.8985 (m-80) REVERT: C 277 TYR cc_start: 0.8335 (p90) cc_final: 0.7448 (p90) REVERT: C 286 MET cc_start: 0.8624 (mmm) cc_final: 0.8241 (ttp) REVERT: C 298 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8485 (tm-30) REVERT: D 14 GLU cc_start: 0.8838 (pt0) cc_final: 0.8514 (pp20) REVERT: D 18 LYS cc_start: 0.9203 (mtmm) cc_final: 0.8744 (mtmm) REVERT: D 165 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8253 (mp0) REVERT: D 182 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8230 (mm-30) REVERT: D 220 TYR cc_start: 0.8567 (t80) cc_final: 0.8163 (t80) REVERT: D 223 LEU cc_start: 0.8909 (mt) cc_final: 0.8586 (pp) REVERT: D 227 MET cc_start: 0.8715 (mmt) cc_final: 0.8413 (mmm) REVERT: D 243 ASN cc_start: 0.6956 (t0) cc_final: 0.6460 (t0) REVERT: E 123 ASP cc_start: 0.9182 (p0) cc_final: 0.8889 (p0) REVERT: E 134 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.7789 (m-80) REVERT: E 140 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8442 (mm-30) REVERT: E 170 LYS cc_start: 0.8216 (mttt) cc_final: 0.7576 (mmmt) REVERT: E 222 THR cc_start: 0.8972 (m) cc_final: 0.8634 (p) REVERT: E 290 MET cc_start: 0.8871 (mmm) cc_final: 0.7595 (mmm) REVERT: K 1 GLN cc_start: 0.8475 (pm20) cc_final: 0.8046 (pm20) REVERT: K 440 TRP cc_start: 0.8542 (m100) cc_final: 0.8274 (m100) REVERT: K 482 TYR cc_start: 0.8310 (m-10) cc_final: 0.8101 (m-10) REVERT: L 459 ARG cc_start: 0.8284 (pmt-80) cc_final: 0.8073 (pmt-80) REVERT: L 474 LYS cc_start: 0.8766 (mttt) cc_final: 0.7931 (mtmt) REVERT: L 504 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7983 (pm20) REVERT: M 3 GLN cc_start: 0.8752 (mp10) cc_final: 0.8501 (mp10) REVERT: M 430 LYS cc_start: 0.9016 (mtpt) cc_final: 0.8631 (tptm) REVERT: M 469 GLU cc_start: 0.8113 (mp0) cc_final: 0.7744 (mp0) REVERT: M 482 TYR cc_start: 0.8749 (m-80) cc_final: 0.8448 (m-80) outliers start: 47 outliers final: 32 residues processed: 369 average time/residue: 0.1278 time to fit residues: 72.9619 Evaluate side-chains 358 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 322 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 292 VAL 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 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 285 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 103 LYS 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 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 K residue 509 THR Chi-restraints excluded: chain L residue 3 GLN 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 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: 5.9990 chunk 191 optimal weight: 8.9990 chunk 158 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 464 ASN L 504 GLN ** M 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.092677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.064731 restraints weight = 230859.702| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 6.94 r_work: 0.2767 rms_B_bonded: 5.91 restraints_weight: 2.0000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 17328 Z= 0.192 Angle : 0.666 20.804 23680 Z= 0.332 Chirality : 0.045 0.294 2691 Planarity : 0.003 0.031 2900 Dihedral : 4.357 23.032 2335 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.86 % Allowed : 16.23 % Favored : 80.91 % 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: 1.44 (0.19), residues: 2024 helix: 1.84 (0.21), residues: 585 sheet: 1.09 (0.22), residues: 559 loop : 0.36 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 207 TYR 0.024 0.002 TYR B 299 PHE 0.026 0.002 PHE A 289 TRP 0.024 0.001 TRP A 237 HIS 0.007 0.001 HIS E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (17291) covalent geometry : angle 0.66174 / 0.33 (23577) SS BOND : bond 0.00171 / 0.13 ( 8) SS BOND : angle 0.32094 / 0.24 ( 16) hydrogen bonds : bond 0.03940 / 2.57 ( 826) hydrogen bonds : angle 4.62500 / 3.30 ( 2623) link_ALPHA1-3 : bond 0.00271 / 0.17 ( 4) link_ALPHA1-3 : angle 1.49074 / 1.10 ( 12) link_ALPHA1-6 : bond 0.00257 / 0.16 ( 4) link_ALPHA1-6 : angle 1.42903 / 1.09 ( 12) link_BETA1-4 : bond 0.00290 / 0.16 ( 12) link_BETA1-4 : angle 1.65467 / 1.16 ( 36) link_NAG-ASN : bond 0.00205 / 0.13 ( 9) link_NAG-ASN : angle 1.23315 / 0.90 ( 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 379 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 330 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6491 (mtp) cc_final: 0.5888 (mpp) REVERT: A 227 MET cc_start: 0.8758 (ttt) cc_final: 0.8421 (ttp) REVERT: A 286 MET cc_start: 0.8774 (mmm) cc_final: 0.8465 (mmm) REVERT: A 429 ILE cc_start: 0.9053 (tp) cc_final: 0.8738 (mm) REVERT: A 445 TYR cc_start: 0.8159 (t80) cc_final: 0.7948 (t80) REVERT: B 286 MET cc_start: 0.8119 (ttp) cc_final: 0.7847 (tmm) REVERT: B 306 PHE cc_start: 0.8086 (t80) cc_final: 0.7846 (t80) REVERT: B 437 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8739 (mp) REVERT: C 18 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8688 (ptpp) REVERT: C 55 MET cc_start: 0.9416 (mmt) cc_final: 0.8737 (mmt) REVERT: C 68 ARG cc_start: 0.8856 (ttt180) cc_final: 0.8527 (ttm-80) REVERT: C 95 ASP cc_start: 0.9138 (p0) cc_final: 0.8927 (p0) REVERT: C 141 ARG cc_start: 0.8744 (mtt90) cc_final: 0.8439 (mtp180) REVERT: C 226 TYR cc_start: 0.9218 (m-80) cc_final: 0.8920 (m-80) REVERT: C 227 MET cc_start: 0.8963 (tpp) cc_final: 0.8705 (tpp) REVERT: C 298 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8489 (tm-30) REVERT: D 13 LYS cc_start: 0.9151 (tttt) cc_final: 0.8806 (tptm) REVERT: D 14 GLU cc_start: 0.8868 (pt0) cc_final: 0.8542 (pp20) REVERT: D 18 LYS cc_start: 0.9191 (mtmm) cc_final: 0.8756 (mtmm) REVERT: D 180 ARG cc_start: 0.7609 (mmp80) cc_final: 0.7290 (mmp80) REVERT: D 182 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8175 (mm-30) REVERT: D 220 TYR cc_start: 0.8418 (t80) cc_final: 0.7962 (t80) REVERT: D 223 LEU cc_start: 0.8907 (mt) cc_final: 0.8532 (pp) REVERT: D 227 MET cc_start: 0.8674 (mmt) cc_final: 0.8319 (mmm) REVERT: D 243 ASN cc_start: 0.7163 (t0) cc_final: 0.6693 (t0) REVERT: E 123 ASP cc_start: 0.9112 (p0) cc_final: 0.8877 (p0) REVERT: E 134 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: E 140 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8424 (mm-30) REVERT: E 170 LYS cc_start: 0.8357 (mttt) cc_final: 0.7762 (mmmt) REVERT: E 177 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7714 (tt0) REVERT: E 222 THR cc_start: 0.8968 (m) cc_final: 0.8728 (p) REVERT: K 1 GLN cc_start: 0.8377 (pm20) cc_final: 0.8094 (pm20) REVERT: K 440 TRP cc_start: 0.8474 (m100) cc_final: 0.8255 (m100) REVERT: K 469 GLU cc_start: 0.7673 (mp0) cc_final: 0.7118 (mp0) REVERT: K 482 TYR cc_start: 0.8474 (m-10) cc_final: 0.8188 (m-10) REVERT: M 4 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8545 (mt) REVERT: M 421 MET cc_start: 0.9140 (mmm) cc_final: 0.8585 (mmm) REVERT: M 430 LYS cc_start: 0.8919 (mtpt) cc_final: 0.8612 (tptp) outliers start: 49 outliers final: 37 residues processed: 357 average time/residue: 0.1276 time to fit residues: 70.0370 Evaluate side-chains 362 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 320 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 292 VAL 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 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 25 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 198 VAL 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 87 MET Chi-restraints excluded: chain E residue 134 PHE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 177 GLU 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 K residue 509 THR Chi-restraints excluded: chain L residue 3 GLN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 133 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 113 optimal weight: 0.1980 chunk 91 optimal weight: 4.9990 chunk 58 optimal weight: 0.0970 chunk 140 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 134 optimal weight: 8.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 200 GLN ** E 253 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 = 0.3590 r_free = 0.3590 target = 0.094005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.065961 restraints weight = 229011.698| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 7.01 r_work: 0.2800 rms_B_bonded: 5.99 restraints_weight: 2.0000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.4691 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= 0.129 Angle : 0.660 18.273 23680 Z= 0.325 Chirality : 0.044 0.252 2691 Planarity : 0.003 0.032 2900 Dihedral : 4.252 23.988 2335 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.36 % Allowed : 16.79 % Favored : 80.85 % 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: 1.41 (0.19), residues: 2024 helix: 1.73 (0.21), residues: 585 sheet: 1.14 (0.22), residues: 559 loop : 0.37 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 141 TYR 0.029 0.001 TYR A 66 PHE 0.028 0.001 PHE A 289 TRP 0.026 0.001 TRP A 237 HIS 0.001 0.000 HIS B 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (17291) covalent geometry : angle 0.65667 / 0.32 (23577) SS BOND : bond 0.00137 / 0.10 ( 8) SS BOND : angle 0.39241 / 0.28 ( 16) hydrogen bonds : bond 0.03823 / 2.49 ( 826) hydrogen bonds : angle 4.55245 / 3.24 ( 2623) link_ALPHA1-3 : bond 0.00346 / 0.21 ( 4) link_ALPHA1-3 : angle 1.42944 / 1.05 ( 12) link_ALPHA1-6 : bond 0.00294 / 0.18 ( 4) link_ALPHA1-6 : angle 1.44459 / 1.07 ( 12) link_BETA1-4 : bond 0.00299 / 0.19 ( 12) link_BETA1-4 : angle 1.47650 / 1.06 ( 36) link_NAG-ASN : bond 0.00122 / 0.08 ( 9) link_NAG-ASN : angle 1.08908 / 0.80 ( 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 381 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 341 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6452 (mtp) cc_final: 0.5795 (mpp) REVERT: A 227 MET cc_start: 0.8729 (ttt) cc_final: 0.8513 (ttp) REVERT: A 286 MET cc_start: 0.8774 (mmm) cc_final: 0.8443 (mmm) REVERT: A 429 ILE cc_start: 0.9016 (tp) cc_final: 0.8715 (mm) REVERT: B 18 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8972 (mtmt) REVERT: B 55 MET cc_start: 0.9251 (mmt) cc_final: 0.9013 (mmt) REVERT: B 227 MET cc_start: 0.9202 (tpp) cc_final: 0.8944 (mmm) REVERT: B 286 MET cc_start: 0.8086 (ttp) cc_final: 0.7801 (tmm) REVERT: B 437 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8734 (mp) REVERT: C 18 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8796 (pttm) REVERT: C 55 MET cc_start: 0.9414 (mmt) cc_final: 0.8729 (mmt) REVERT: C 141 ARG cc_start: 0.8717 (mtt90) cc_final: 0.8420 (mtp180) REVERT: C 226 TYR cc_start: 0.9221 (m-80) cc_final: 0.8913 (m-80) REVERT: C 227 MET cc_start: 0.8906 (tpp) cc_final: 0.8616 (tpp) REVERT: C 298 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8396 (tm-30) REVERT: D 13 LYS cc_start: 0.9171 (tttt) cc_final: 0.8806 (tptm) REVERT: D 14 GLU cc_start: 0.8900 (pt0) cc_final: 0.8566 (pp20) REVERT: D 18 LYS cc_start: 0.9174 (mtmm) cc_final: 0.8746 (mtmm) REVERT: D 180 ARG cc_start: 0.7576 (mmp80) cc_final: 0.7284 (mmp80) REVERT: D 182 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8183 (mm-30) REVERT: D 227 MET cc_start: 0.8632 (mmt) cc_final: 0.8357 (tpp) REVERT: D 243 ASN cc_start: 0.7147 (t0) cc_final: 0.6723 (t0) REVERT: D 298 GLU cc_start: 0.9125 (tm-30) cc_final: 0.8842 (tm-30) REVERT: E 123 ASP cc_start: 0.9090 (p0) cc_final: 0.8866 (p0) REVERT: E 134 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.7732 (m-80) REVERT: E 140 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8372 (mm-30) REVERT: E 170 LYS cc_start: 0.8303 (mttt) cc_final: 0.7718 (mmmt) REVERT: E 179 MET cc_start: 0.8592 (mmm) cc_final: 0.8187 (mmm) REVERT: K 1 GLN cc_start: 0.8393 (pm20) cc_final: 0.8117 (pm20) REVERT: K 469 GLU cc_start: 0.7697 (mp0) cc_final: 0.7081 (mp0) REVERT: K 482 TYR cc_start: 0.8396 (m-10) cc_final: 0.8119 (m-10) REVERT: L 460 ASP cc_start: 0.8209 (t0) cc_final: 0.7852 (p0) REVERT: L 504 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7886 (pm20) REVERT: M 421 MET cc_start: 0.9134 (mmm) cc_final: 0.8680 (mmm) REVERT: M 469 GLU cc_start: 0.7824 (mp0) cc_final: 0.7617 (mp0) outliers start: 40 outliers final: 31 residues processed: 358 average time/residue: 0.1351 time to fit residues: 73.7888 Evaluate side-chains 359 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 323 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 194 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 302 VAL 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 25 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 115 MET 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 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 415 THR 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 3 GLN 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 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: 7.9990 chunk 61 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN 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 = 0.3558 r_free = 0.3558 target = 0.092366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.064617 restraints weight = 248148.326| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 7.06 r_work: 0.2755 rms_B_bonded: 6.03 restraints_weight: 2.0000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17328 Z= 0.225 Angle : 0.709 17.199 23680 Z= 0.353 Chirality : 0.046 0.269 2691 Planarity : 0.004 0.062 2900 Dihedral : 4.421 23.880 2335 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.75 % Allowed : 17.29 % 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: 1.28 (0.19), residues: 2024 helix: 1.61 (0.21), residues: 585 sheet: 1.11 (0.22), residues: 556 loop : 0.27 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 96 TYR 0.034 0.002 TYR A 66 PHE 0.032 0.002 PHE A 289 TRP 0.024 0.002 TRP L 440 HIS 0.005 0.001 HIS E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.23 (17291) covalent geometry : angle 0.70424 / 0.35 (23577) SS BOND : bond 0.00194 / 0.14 ( 8) SS BOND : angle 0.43341 / 0.34 ( 16) hydrogen bonds : bond 0.03989 / 2.60 ( 826) hydrogen bonds : angle 4.68839 / 3.35 ( 2623) link_ALPHA1-3 : bond 0.00236 / 0.15 ( 4) link_ALPHA1-3 : angle 1.52197 / 1.12 ( 12) link_ALPHA1-6 : bond 0.00227 / 0.14 ( 4) link_ALPHA1-6 : angle 1.43587 / 1.10 ( 12) link_BETA1-4 : bond 0.00317 / 0.18 ( 12) link_BETA1-4 : angle 1.73956 / 1.22 ( 36) link_NAG-ASN : bond 0.00274 / 0.17 ( 9) link_NAG-ASN : angle 1.28894 / 0.95 ( 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 371 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 324 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6393 (mtp) cc_final: 0.5886 (mpp) REVERT: A 227 MET cc_start: 0.8787 (ttt) cc_final: 0.8494 (ttp) REVERT: A 286 MET cc_start: 0.8794 (mmm) cc_final: 0.8462 (mmm) REVERT: A 429 ILE cc_start: 0.9046 (tp) cc_final: 0.8732 (mm) REVERT: B 18 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8885 (mtpt) REVERT: B 55 MET cc_start: 0.9219 (mmt) cc_final: 0.8927 (mmt) REVERT: B 227 MET cc_start: 0.9173 (tpp) cc_final: 0.8921 (mmm) REVERT: B 286 MET cc_start: 0.8176 (ttp) cc_final: 0.7903 (tmm) REVERT: B 437 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8731 (mp) REVERT: C 18 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8778 (pttm) REVERT: C 55 MET cc_start: 0.9424 (mmt) cc_final: 0.8746 (mmt) REVERT: C 141 ARG cc_start: 0.8753 (mtt90) cc_final: 0.8467 (mtp180) REVERT: C 226 TYR cc_start: 0.9232 (m-80) cc_final: 0.8939 (m-80) REVERT: C 227 MET cc_start: 0.8958 (tpp) cc_final: 0.8702 (tpp) REVERT: D 13 LYS cc_start: 0.9180 (tttt) cc_final: 0.8840 (tptm) REVERT: D 14 GLU cc_start: 0.8872 (pt0) cc_final: 0.8556 (pp20) REVERT: D 18 LYS cc_start: 0.9223 (mtmm) cc_final: 0.8807 (mtmm) REVERT: D 182 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8218 (mm-30) REVERT: D 227 MET cc_start: 0.8615 (mmt) cc_final: 0.8309 (mmm) REVERT: D 243 ASN cc_start: 0.7187 (t0) cc_final: 0.6750 (t0) REVERT: E 134 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.7747 (m-80) REVERT: E 140 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8438 (mm-30) REVERT: E 170 LYS cc_start: 0.8426 (mttt) cc_final: 0.7858 (mmmt) REVERT: E 179 MET cc_start: 0.8633 (mmm) cc_final: 0.8264 (mmm) REVERT: K 1 GLN cc_start: 0.8393 (pm20) cc_final: 0.8146 (pm20) REVERT: K 449 ASP cc_start: 0.9210 (p0) cc_final: 0.9003 (p0) REVERT: K 469 GLU cc_start: 0.7785 (mp0) cc_final: 0.7174 (mp0) REVERT: K 482 TYR cc_start: 0.8505 (m-10) cc_final: 0.8144 (m-10) REVERT: L 6 GLU cc_start: 0.8306 (pm20) cc_final: 0.8061 (pm20) REVERT: L 460 ASP cc_start: 0.8084 (t0) cc_final: 0.7681 (p0) REVERT: M 421 MET cc_start: 0.9148 (mmm) cc_final: 0.8669 (mmm) REVERT: M 474 LYS cc_start: 0.9034 (mttt) cc_final: 0.8438 (mttt) outliers start: 47 outliers final: 36 residues processed: 349 average time/residue: 0.1252 time to fit residues: 67.3275 Evaluate side-chains 352 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 312 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 160 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 18 LYS 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 25 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 115 MET 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 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 415 THR 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 3 GLN 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 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 Chi-restraints excluded: chain M residue 497 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 73 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.090738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.063267 restraints weight = 228672.207| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 6.73 r_work: 0.2731 rms_B_bonded: 5.85 restraints_weight: 2.0000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.132 17328 Z= 0.277 Angle : 0.750 16.560 23680 Z= 0.379 Chirality : 0.047 0.247 2691 Planarity : 0.004 0.035 2900 Dihedral : 4.731 31.582 2335 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.75 % Allowed : 17.46 % Favored : 79.79 % 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: 1.02 (0.19), residues: 2024 helix: 1.46 (0.21), residues: 585 sheet: 0.88 (0.22), residues: 556 loop : 0.12 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 207 TYR 0.028 0.002 TYR B 299 PHE 0.037 0.002 PHE A 289 TRP 0.035 0.002 TRP L 440 HIS 0.006 0.001 HIS E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.28 (17291) covalent geometry : angle 0.74414 / 0.38 (23577) SS BOND : bond 0.00230 / 0.16 ( 8) SS BOND : angle 0.55801 / 0.41 ( 16) hydrogen bonds : bond 0.04227 / 2.75 ( 826) hydrogen bonds : angle 4.86379 / 3.46 ( 2623) link_ALPHA1-3 : bond 0.00198 / 0.13 ( 4) link_ALPHA1-3 : angle 1.59185 / 1.17 ( 12) link_ALPHA1-6 : bond 0.00173 / 0.11 ( 4) link_ALPHA1-6 : angle 1.46448 / 1.14 ( 12) link_BETA1-4 : bond 0.00410 / 0.25 ( 12) link_BETA1-4 : angle 1.88292 / 1.31 ( 36) link_NAG-ASN : bond 0.00408 / 0.26 ( 9) link_NAG-ASN : angle 1.46937 / 1.08 ( 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 371 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 324 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6333 (mtp) cc_final: 0.5738 (mpp) REVERT: A 55 MET cc_start: 0.8189 (tpp) cc_final: 0.7798 (tpp) REVERT: A 227 MET cc_start: 0.8794 (ttt) cc_final: 0.8498 (ttp) REVERT: A 429 ILE cc_start: 0.9071 (tp) cc_final: 0.8763 (mm) REVERT: B 55 MET cc_start: 0.9220 (mmt) cc_final: 0.8926 (mmt) REVERT: B 227 MET cc_start: 0.9166 (tpp) cc_final: 0.8912 (mmm) REVERT: B 286 MET cc_start: 0.8221 (ttp) cc_final: 0.7896 (tmm) REVERT: B 437 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8723 (mp) REVERT: C 18 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8739 (pttm) REVERT: C 55 MET cc_start: 0.9433 (mmt) cc_final: 0.8748 (mmt) REVERT: C 141 ARG cc_start: 0.8755 (mtt90) cc_final: 0.8474 (mtp180) REVERT: C 227 MET cc_start: 0.8965 (tpp) cc_final: 0.8723 (tpp) REVERT: D 13 LYS cc_start: 0.9200 (tttt) cc_final: 0.8861 (tptm) REVERT: D 14 GLU cc_start: 0.8886 (pt0) cc_final: 0.8591 (pp20) REVERT: D 18 LYS cc_start: 0.9251 (mtmm) cc_final: 0.8911 (mtmm) REVERT: D 180 ARG cc_start: 0.7663 (mmp80) cc_final: 0.7294 (mmp80) REVERT: D 243 ASN cc_start: 0.7255 (t0) cc_final: 0.6824 (t0) REVERT: E 83 MET cc_start: 0.8737 (mmm) cc_final: 0.8508 (mmm) REVERT: E 134 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.7798 (m-80) REVERT: E 140 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8431 (mm-30) REVERT: E 170 LYS cc_start: 0.8457 (mttt) cc_final: 0.7917 (mmmt) REVERT: E 177 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: E 179 MET cc_start: 0.8761 (mmm) cc_final: 0.8303 (mmm) REVERT: E 308 LYS cc_start: 0.7138 (mtmm) cc_final: 0.6927 (mtpp) REVERT: E 333 PHE cc_start: 0.8580 (t80) cc_final: 0.7990 (t80) REVERT: K 469 GLU cc_start: 0.8069 (mp0) cc_final: 0.7401 (mp0) REVERT: K 482 TYR cc_start: 0.8605 (m-10) cc_final: 0.8230 (m-10) REVERT: L 460 ASP cc_start: 0.8208 (t0) cc_final: 0.7763 (p0) REVERT: M 421 MET cc_start: 0.9152 (mmm) cc_final: 0.8708 (mmm) REVERT: M 431 GLU cc_start: 0.8225 (tp30) cc_final: 0.7970 (pm20) REVERT: M 463 LYS cc_start: 0.8731 (ptpp) cc_final: 0.8494 (ptmm) outliers start: 47 outliers final: 36 residues processed: 347 average time/residue: 0.1223 time to fit residues: 65.9813 Evaluate side-chains 351 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 311 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 160 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 292 VAL 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 25 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 115 MET 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 87 MET Chi-restraints excluded: chain E residue 134 PHE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 177 GLU 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 K residue 509 THR Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 431 GLU 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 M residue 2 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 414 HIS Chi-restraints excluded: chain M residue 464 ASN Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 497 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 181 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 2 optimal weight: 0.0040 chunk 13 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 172 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** L 504 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.092074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.064237 restraints weight = 232154.946| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 7.09 r_work: 0.2733 rms_B_bonded: 6.09 restraints_weight: 2.0000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 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 = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17328 Z= 0.130 Angle : 0.712 17.063 23680 Z= 0.350 Chirality : 0.045 0.276 2691 Planarity : 0.003 0.032 2900 Dihedral : 4.407 23.499 2335 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.57 % Allowed : 18.98 % Favored : 79.45 % 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: 1.11 (0.19), residues: 2024 helix: 1.43 (0.21), residues: 585 sheet: 0.98 (0.22), residues: 554 loop : 0.22 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 96 TYR 0.020 0.002 TYR D 299 PHE 0.034 0.002 PHE A 289 TRP 0.025 0.001 TRP A 237 HIS 0.002 0.000 HIS E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (17291) covalent geometry : angle 0.70824 / 0.35 (23577) SS BOND : bond 0.00147 / 0.10 ( 8) SS BOND : angle 0.34236 / 0.26 ( 16) hydrogen bonds : bond 0.03917 / 2.55 ( 826) hydrogen bonds : angle 4.63732 / 3.29 ( 2623) link_ALPHA1-3 : bond 0.00381 / 0.22 ( 4) link_ALPHA1-3 : angle 1.44867 / 1.07 ( 12) link_ALPHA1-6 : bond 0.00274 / 0.17 ( 4) link_ALPHA1-6 : angle 1.53120 / 1.12 ( 12) link_BETA1-4 : bond 0.00266 / 0.16 ( 12) link_BETA1-4 : angle 1.48035 / 1.07 ( 36) link_NAG-ASN : bond 0.00193 / 0.12 ( 9) link_NAG-ASN : angle 1.06644 / 0.80 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4752.99 seconds wall clock time: 82 minutes 14.16 seconds (4934.16 seconds total)