Starting phenix.real_space_refine on Fri Jul 3 21:30:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qn5_14067/07_2026/7qn5_14067.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qn5_14067/07_2026/7qn5_14067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qn5_14067/07_2026/7qn5_14067.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qn5_14067/07_2026/7qn5_14067.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7qn5_14067/07_2026/7qn5_14067.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qn5_14067/07_2026/7qn5_14067.cif" model { file = "/net/cci-nas-00/data/ceres_data/7qn5_14067/07_2026/7qn5_14067.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qn5_14067/07_2026/7qn5_14067.cif" } resolution = 2.5 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 93 5.16 5 Cl 3 4.86 5 C 10335 2.51 5 N 2531 2.21 5 O 3085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s 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: 16048 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2711 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 318} Chain breaks: 1 Chain: "B" Number of atoms: 2737 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: 2697 Chain: "C" Number of atoms: 2759 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: 2673 Chain: "D" Number of atoms: 2709 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: 2730 Chain: "E" Number of atoms: 2595 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 323, 2584 Classifications: {'peptide': 323} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 310} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 323, 2584 Classifications: {'peptide': 323} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 310} Chain breaks: 1 bond proxies already assigned to first conformer: 2641 Chain: "F" 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: "G" 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: 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: "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: "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: "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: "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: "J" 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: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 76 Unusual residues: {'D10': 1, 'NAG': 1, 'OCT': 1, 'PX6': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 17 Unusual residues: {' CL': 2, 'EPE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'EPE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 47 Unusual residues: {' CL': 1, 'D10': 1, 'NAG': 2, 'OCT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N ATYR B 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B 66 " 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 AILE C 164 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE C 164 " 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 ALEU C 214 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU C 214 " occ=0.50 residue: pdb=" N ATYR D 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR D 66 " occ=0.50 Time building chain proxies: 5.20, per 1000 atoms: 0.32 Number of scatterers: 16048 At special positions: 0 Unit cell: (117.376, 120.064, 136.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 3 17.00 S 93 16.00 P 1 15.00 O 3085 8.00 N 2531 7.00 C 10335 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 186 " 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 F 409 " - pdb=" SG CYS F 483 " distance=2.03 Simple disulfide: pdb=" SG CYS G 409 " - pdb=" SG CYS G 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 H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 5 " " BMA a 3 " - " MAN a 5 " BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A 601 " - " ASN A 157 " " NAG E 502 " - " ASN E 65 " " NAG E 503 " - " ASN E 103 " " NAG H 1 " - " ASN B 149 " " NAG I 1 " - " ASN C 149 " " NAG J 1 " - " ASN D 149 " " NAG a 1 " - " ASN A 144 " " NAG b 1 " - " ASN B 80 " " NAG c 1 " - " ASN C 80 " " NAG d 1 " - " ASN D 80 " Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 1.0 seconds 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3582 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 21 sheets defined 37.7% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 106 through 109 Processing helix chain 'A' and resid 120 through 127 removed outlier: 3.553A pdb=" N THR A 125 " --> pdb=" O MET A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 179 removed outlier: 4.569A pdb=" N ASP A 178 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 219 Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 263 through 277 removed outlier: 4.142A pdb=" N SER A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 284 through 310 removed outlier: 4.422A pdb=" N SER A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 349 removed outlier: 3.592A pdb=" N ILE A 346 " --> pdb=" O TYR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 544 removed outlier: 3.836A pdb=" N ILE A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Proline residue: A 527 - end of helix removed outlier: 3.800A pdb=" N LYS A 544 " --> pdb=" O VAL A 540 " (cutoff:3.500A) 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 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 Processing helix chain 'B' and resid 225 through 238 removed outlier: 3.543A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 242 Processing helix chain 'B' and resid 246 through 270 Processing helix chain 'B' and resid 279 through 307 removed outlier: 3.880A pdb=" N PHE B 307 " --> pdb=" O ASN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 447 removed outlier: 3.517A 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 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 Processing helix chain 'C' and resid 225 through 238 removed outlier: 3.544A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 242 Processing helix chain 'C' and resid 246 through 270 Processing helix chain 'C' and resid 279 through 307 removed outlier: 3.880A pdb=" N PHE C 307 " --> pdb=" O ASN C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 447 removed outlier: 3.517A 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 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 Processing helix chain 'D' and resid 225 through 238 removed outlier: 3.543A pdb=" N TRP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 242 Processing helix chain 'D' and resid 246 through 270 Processing helix chain 'D' and resid 279 through 307 removed outlier: 3.880A pdb=" N PHE D 307 " --> pdb=" O ASN D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 447 removed outlier: 3.517A 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 43 through 49 Processing helix chain 'E' and resid 98 through 101 Processing helix chain 'E' and resid 112 through 119 removed outlier: 3.547A pdb=" N PHE E 115 " --> pdb=" O ASP E 112 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP E 117 " --> pdb=" O ARG E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 removed outlier: 3.573A pdb=" N HIS E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 271 Proline residue: E 257 - end of helix removed outlier: 3.593A pdb=" N VAL E 267 " --> pdb=" O ALA E 263 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER E 268 " --> pdb=" O MET E 264 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE E 269 " --> pdb=" O SER E 265 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TRP E 270 " --> pdb=" O TRP E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 300 removed outlier: 3.531A pdb=" N THR E 286 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG E 298 " --> pdb=" O MET E 294 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER E 300 " --> pdb=" O SER E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 335 Processing helix chain 'E' and resid 425 through 450 removed outlier: 3.502A pdb=" N ILE E 429 " --> pdb=" O ASP E 425 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA E 433 " --> pdb=" O ILE E 429 " (cutoff:3.500A) Proline residue: E 436 - end of helix Processing helix chain 'F' and resid 449 through 452 Processing helix chain 'F' and resid 495 through 497 No H-bonds generated for 'chain 'F' and resid 495 through 497' Processing helix chain 'G' and resid 449 through 452 Processing helix chain 'G' and resid 495 through 497 No H-bonds generated for 'chain 'G' and resid 495 through 497' Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 119 removed outlier: 4.733A pdb=" N PHE A 152 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR A 159 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLU A 92 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR A 94 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N PHE A 83 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP A 96 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE A 104 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLU A 73 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR A 72 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N THR A 203 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL A 74 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 142 removed outlier: 6.620A pdb=" N GLY A 137 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU A 171 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLU A 92 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR A 94 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N PHE A 83 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP A 96 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE A 104 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLU A 73 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N GLU A 213 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 78 " --> pdb=" O GLU A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 134 removed outlier: 4.336A pdb=" N SER A 192 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE A 244 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 228 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG A 253 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU A 226 " --> pdb=" O ARG A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 83 removed outlier: 4.263A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.420A 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: 6.662A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.543A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 81 through 83 removed outlier: 4.263A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.431A 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: 6.662A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.543A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 81 through 83 removed outlier: 4.263A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.433A 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: 6.662A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL D 106 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ARG D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.543A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.725A 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: 6.131A pdb=" N ALA E 163 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 6.171A 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: 5.671A pdb=" N GLU E 84 " --> pdb=" O HIS E 77 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS E 77 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR E 86 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE E 75 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR E 88 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ARG E 96 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN E 65 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL E 64 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N TYR E 195 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 6.152A 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: 4.036A pdb=" N SER E 218 " --> pdb=" O HIS E 242 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG E 244 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE E 216 " --> pdb=" O ARG E 244 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 2 through 7 Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.695A pdb=" N GLY F 10 " --> pdb=" O GLN F 507 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR F 509 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE F 420 " --> pdb=" O LYS F 486 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ARG F 425 " --> pdb=" O PHE F 434 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N PHE F 434 " --> pdb=" O ARG F 425 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.695A pdb=" N GLY F 10 " --> pdb=" O GLN F 507 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR F 509 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N CYS F 483 " --> pdb=" O TRP F 502 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TRP F 502 " --> pdb=" O CYS F 483 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA F 485 " --> pdb=" O ASP F 500 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 2 through 7 Processing sheet with id=AC2, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.695A pdb=" N GLY G 10 " --> pdb=" O GLN G 507 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR G 509 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE G 420 " --> pdb=" O LYS G 486 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ARG G 425 " --> pdb=" O PHE G 434 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N PHE G 434 " --> pdb=" O ARG G 425 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.695A pdb=" N GLY G 10 " --> pdb=" O GLN G 507 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR G 509 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS G 483 " --> pdb=" O TRP G 502 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TRP G 502 " --> pdb=" O CYS G 483 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA G 485 " --> pdb=" O ASP G 500 " (cutoff:3.500A) 908 hydrogen bonds defined for protein. 2530 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: 3.02 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2546 1.32 - 1.45: 4771 1.45 - 1.57: 8821 1.57 - 1.69: 1 1.69 - 1.81: 161 Bond restraints: 16300 Sorted by residual: bond pdb=" O4 PX6 A 602 " pdb=" P1 PX6 A 602 " ideal model delta sigma weight residual 1.705 1.597 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C1 PX6 A 602 " pdb=" O4 PX6 A 602 " ideal model delta sigma weight residual 1.387 1.443 -0.056 2.00e-02 2.50e+03 7.81e+00 bond pdb=" C10 EPE D 501 " pdb=" S EPE D 501 " ideal model delta sigma weight residual 1.804 1.765 0.039 2.00e-02 2.50e+03 3.75e+00 bond pdb=" C10 EPE C 501 " pdb=" S EPE C 501 " ideal model delta sigma weight residual 1.804 1.766 0.038 2.00e-02 2.50e+03 3.54e+00 bond pdb=" O3S EPE C 501 " pdb=" S EPE C 501 " ideal model delta sigma weight residual 1.477 1.443 0.034 2.00e-02 2.50e+03 2.93e+00 ... (remaining 16295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 21275 1.28 - 2.55: 697 2.55 - 3.83: 146 3.83 - 5.11: 43 5.11 - 6.39: 6 Bond angle restraints: 22167 Sorted by residual: angle pdb=" C TYR B 304 " pdb=" N ILE B 305 " pdb=" CA ILE B 305 " ideal model delta sigma weight residual 121.85 117.69 4.16 1.19e+00 7.06e-01 1.22e+01 angle pdb=" C TYR C 304 " pdb=" N ILE C 305 " pdb=" CA ILE C 305 " ideal model delta sigma weight residual 121.85 117.70 4.15 1.19e+00 7.06e-01 1.22e+01 angle pdb=" C TYR D 304 " pdb=" N ILE D 305 " pdb=" CA ILE D 305 " ideal model delta sigma weight residual 121.85 117.73 4.12 1.19e+00 7.06e-01 1.20e+01 angle pdb=" N PHE C 306 " pdb=" CA PHE C 306 " pdb=" C PHE C 306 " ideal model delta sigma weight residual 111.82 107.88 3.94 1.16e+00 7.43e-01 1.15e+01 angle pdb=" N PHE D 306 " pdb=" CA PHE D 306 " pdb=" C PHE D 306 " ideal model delta sigma weight residual 111.82 107.93 3.89 1.16e+00 7.43e-01 1.13e+01 ... (remaining 22162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.61: 9060 23.61 - 47.23: 242 47.23 - 70.84: 17 70.84 - 94.46: 12 94.46 - 118.07: 10 Dihedral angle restraints: 9341 sinusoidal: 3729 harmonic: 5612 Sorted by residual: dihedral pdb=" CA SER C 46 " pdb=" C SER C 46 " pdb=" N ILE C 47 " pdb=" CA ILE C 47 " ideal model delta harmonic sigma weight residual 180.00 154.72 25.28 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA SER D 46 " pdb=" C SER D 46 " pdb=" N ILE D 47 " pdb=" CA ILE D 47 " ideal model delta harmonic sigma weight residual 180.00 154.74 25.26 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA SER B 46 " pdb=" C SER B 46 " pdb=" N ILE B 47 " pdb=" CA ILE B 47 " ideal model delta harmonic sigma weight residual 180.00 154.78 25.22 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 9338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2155 0.060 - 0.119: 347 0.119 - 0.178: 22 0.178 - 0.238: 5 0.238 - 0.297: 6 Chirality restraints: 2535 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.35e+01 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 6.91e+01 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.77e+01 ... (remaining 2532 not shown) Planarity restraints: 2714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 157 " 0.011 2.00e-02 2.50e+03 1.66e-02 5.52e+00 pdb=" CG TYR C 157 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR C 157 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR C 157 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 157 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR C 157 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 157 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR C 157 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 157 " -0.011 2.00e-02 2.50e+03 1.66e-02 5.51e+00 pdb=" CG TYR B 157 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR B 157 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B 157 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 157 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR B 157 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 157 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR B 157 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 157 " 0.011 2.00e-02 2.50e+03 1.65e-02 5.46e+00 pdb=" CG TYR D 157 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR D 157 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR D 157 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR D 157 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR D 157 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 157 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR D 157 " 0.022 2.00e-02 2.50e+03 ... (remaining 2711 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4451 2.81 - 3.33: 14701 3.33 - 3.86: 28287 3.86 - 4.38: 34395 4.38 - 4.90: 57032 Nonbonded interactions: 138866 Sorted by model distance: nonbonded pdb=" O VAL D 50 " pdb=" NH2 ARG E 303 " model vdw 2.290 3.120 nonbonded pdb=" O PHE E 439 " pdb=" ND2 ASN E 443 " model vdw 2.298 3.120 nonbonded pdb=" OE1BGLN B 64 " pdb=" O HOH B 501 " model vdw 2.298 3.040 nonbonded pdb=" O PRO A 130 " pdb=" O HOH A 701 " model vdw 2.312 3.040 nonbonded pdb=" O ALA E 52 " pdb=" NH1 ARG E 99 " model vdw 2.319 3.120 ... (remaining 138861 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 'B' and (resid 7 through 40 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 or resid 69 through 111 or resid \ 113 through 124 or resid 126 through 163 or resid 165 through 208 or resid 210 \ through 213 or resid 215 through 240 or resid 242 through 447)) selection = (chain 'C' and (resid 7 through 40 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 or resid 69 through 111 or resid \ 113 through 124 or resid 126 through 163 or resid 165 through 208 or resid 210 \ through 213 or resid 215 through 240 or resid 242 through 447)) selection = (chain 'D' and (resid 7 through 40 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 or resid 69 through 111 or resid \ 113 through 124 or resid 126 through 163 or resid 165 through 208 or resid 210 \ through 213 or resid 215 through 240 or resid 242 through 447)) } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'a' } ncs_group { reference = 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=0.99 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 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: 0.040 Process input model: 18.310 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 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 0.108 16336 Z= 0.152 Angle : 0.577 6.712 22268 Z= 0.295 Chirality : 0.045 0.297 2535 Planarity : 0.005 0.058 2704 Dihedral : 12.036 118.071 5738 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.36 % Allowed : 3.10 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1888 helix: 0.78 (0.20), residues: 570 sheet: 1.07 (0.23), residues: 517 loop : 0.51 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG C 28 TYR 0.022 0.004 TYR B 157 PHE 0.021 0.001 PHE B 221 TRP 0.013 0.001 TRP F 440 HIS 0.002 0.000 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (16300) covalent geometry : angle 0.57078 / 0.29 (22167) SS BOND : bond 0.00142 / 0.07 ( 7) SS BOND : angle 0.67902 / 0.35 ( 14) hydrogen bonds : bond 0.20727 / 13.61 ( 808) hydrogen bonds : angle 7.28787 / 5.19 ( 2530) link_ALPHA1-3 : bond 0.00083 / 0.04 ( 4) link_ALPHA1-3 : angle 0.59342 / 0.33 ( 12) link_ALPHA1-6 : bond 0.00166 / 0.08 ( 4) link_ALPHA1-6 : angle 0.68101 / 0.36 ( 12) link_BETA1-4 : bond 0.00210 / 0.12 ( 11) link_BETA1-4 : angle 1.20840 / 0.75 ( 33) link_NAG-ASN : bond 0.00446 / 0.26 ( 10) link_NAG-ASN : angle 2.12234 / 1.56 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 451 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ASP cc_start: 0.8351 (m-30) cc_final: 0.8075 (m-30) REVERT: B 8 ASN cc_start: 0.7139 (t0) cc_final: 0.6624 (p0) REVERT: B 283 MET cc_start: 0.8483 (mmm) cc_final: 0.8091 (tpp) REVERT: C 8 ASN cc_start: 0.7486 (t0) cc_final: 0.6395 (p0) REVERT: C 137 MET cc_start: 0.8083 (mmp) cc_final: 0.7634 (mmm) REVERT: C 223 LEU cc_start: 0.8458 (mt) cc_final: 0.8227 (tp) REVERT: C 301 PHE cc_start: 0.7510 (t80) cc_final: 0.7262 (t80) REVERT: D 13 LYS cc_start: 0.8545 (tttp) cc_final: 0.8111 (ttmt) REVERT: D 227 MET cc_start: 0.7557 (mmt) cc_final: 0.7119 (tpp) REVERT: D 243 ASN cc_start: 0.7876 (t0) cc_final: 0.7660 (t0) REVERT: D 439 ASN cc_start: 0.8395 (m-40) cc_final: 0.8031 (m-40) REVERT: E 219 TYR cc_start: 0.8690 (p90) cc_final: 0.8449 (p90) REVERT: F 472 ASN cc_start: 0.8035 (t0) cc_final: 0.7676 (t0) REVERT: G 458 SER cc_start: 0.8446 (t) cc_final: 0.8021 (p) REVERT: G 464 ASN cc_start: 0.8145 (m-40) cc_final: 0.7762 (m-40) REVERT: G 473 LEU cc_start: 0.8841 (mt) cc_final: 0.8572 (mm) REVERT: G 490 SER cc_start: 0.8743 (m) cc_final: 0.8510 (p) outliers start: 5 outliers final: 2 residues processed: 454 average time/residue: 0.6020 time to fit residues: 303.0358 Evaluate side-chains 285 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 283 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 275 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN A 275 GLN A 341 ASN A 347 GLN B 185 GLN B 303 ASN ** C 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 HIS E 240 HIS F 3 GLN F 464 ASN F 504 GLN G 426 GLN G 472 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.114283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.074199 restraints weight = 96785.443| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.90 r_work: 0.2698 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9137 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 16336 Z= 0.233 Angle : 0.683 8.014 22268 Z= 0.358 Chirality : 0.047 0.184 2535 Planarity : 0.005 0.037 2704 Dihedral : 8.978 117.567 2216 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 3.10 % Allowed : 13.07 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1888 helix: 1.89 (0.21), residues: 572 sheet: 0.94 (0.22), residues: 531 loop : 0.99 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 213 TYR 0.033 0.002 TYR B 157 PHE 0.033 0.002 PHE E 330 TRP 0.013 0.002 TRP C 168 HIS 0.004 0.001 HIS E 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 (16300) covalent geometry : angle 0.67249 / 0.36 (22167) SS BOND : bond 0.00373 / 0.25 ( 7) SS BOND : angle 0.98792 / 0.57 ( 14) hydrogen bonds : bond 0.04994 / 3.20 ( 808) hydrogen bonds : angle 5.08527 / 3.63 ( 2530) link_ALPHA1-3 : bond 0.00304 / 0.15 ( 4) link_ALPHA1-3 : angle 1.62758 / 0.83 ( 12) link_ALPHA1-6 : bond 0.00529 / 0.27 ( 4) link_ALPHA1-6 : angle 1.36940 / 0.67 ( 12) link_BETA1-4 : bond 0.00490 / 0.32 ( 11) link_BETA1-4 : angle 1.99628 / 1.39 ( 33) link_NAG-ASN : bond 0.00422 / 0.23 ( 10) link_NAG-ASN : angle 2.38125 / 1.68 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 316 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8703 (mp) REVERT: A 91 MET cc_start: 0.9351 (mtt) cc_final: 0.9006 (mtt) REVERT: A 236 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.9088 (pp) REVERT: A 256 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8141 (ttp) REVERT: A 535 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.6979 (mpm) REVERT: B 8 ASN cc_start: 0.7105 (t0) cc_final: 0.6570 (p0) REVERT: B 9 MET cc_start: 0.8256 (mtp) cc_final: 0.8008 (mtp) REVERT: B 21 LYS cc_start: 0.8568 (tppt) cc_final: 0.8356 (tppp) REVERT: B 283 MET cc_start: 0.9042 (mmm) cc_final: 0.8705 (tpp) REVERT: C 49 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7019 (pp-130) REVERT: C 90 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8500 (mt0) REVERT: C 137 MET cc_start: 0.8905 (mmp) cc_final: 0.8591 (mmm) REVERT: C 223 LEU cc_start: 0.8573 (mt) cc_final: 0.8191 (tp) REVERT: C 301 PHE cc_start: 0.7275 (t80) cc_final: 0.7051 (t80) REVERT: D 17 ASP cc_start: 0.8498 (m-30) cc_final: 0.8278 (m-30) REVERT: D 227 MET cc_start: 0.8124 (mmt) cc_final: 0.7875 (tpp) REVERT: D 230 ILE cc_start: 0.9165 (mt) cc_final: 0.8778 (mp) REVERT: D 234 ILE cc_start: 0.9193 (mt) cc_final: 0.8935 (mp) REVERT: D 439 ASN cc_start: 0.8537 (m-40) cc_final: 0.8126 (m-40) REVERT: E 83 MET cc_start: 0.9240 (mmm) cc_final: 0.8997 (mmm) REVERT: E 430 TYR cc_start: 0.8204 (m-80) cc_final: 0.7778 (m-80) REVERT: F 407 LEU cc_start: 0.8589 (tp) cc_final: 0.8380 (mm) REVERT: F 472 ASN cc_start: 0.7846 (t0) cc_final: 0.7553 (t0) REVERT: G 458 SER cc_start: 0.8946 (t) cc_final: 0.8734 (p) REVERT: G 464 ASN cc_start: 0.8194 (m-40) cc_final: 0.7785 (m-40) REVERT: G 472 ASN cc_start: 0.8158 (t0) cc_final: 0.7600 (t0) REVERT: G 473 LEU cc_start: 0.8902 (mt) cc_final: 0.8447 (mm) REVERT: G 474 LYS cc_start: 0.8175 (mptt) cc_final: 0.7797 (mmmt) outliers start: 52 outliers final: 15 residues processed: 339 average time/residue: 0.5468 time to fit residues: 207.0182 Evaluate side-chains 301 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 280 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain E residue 114 ARG Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 450 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 158 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN A 275 GLN ** C 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 ASN ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 1 GLN G 504 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.112294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.072068 restraints weight = 112098.480| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 4.08 r_work: 0.2649 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9183 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 16336 Z= 0.238 Angle : 0.651 10.681 22268 Z= 0.338 Chirality : 0.046 0.219 2535 Planarity : 0.004 0.040 2704 Dihedral : 8.816 121.275 2216 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.81 % Allowed : 14.69 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.72 (0.19), residues: 1888 helix: 1.95 (0.22), residues: 576 sheet: 0.80 (0.22), residues: 526 loop : 0.96 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 50 TYR 0.027 0.002 TYR D 299 PHE 0.031 0.002 PHE E 330 TRP 0.009 0.001 TRP D 426 HIS 0.004 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.24 (16300) covalent geometry : angle 0.63888 / 0.34 (22167) SS BOND : bond 0.00333 / 0.24 ( 7) SS BOND : angle 1.10487 / 0.64 ( 14) hydrogen bonds : bond 0.04742 / 3.06 ( 808) hydrogen bonds : angle 4.91805 / 3.51 ( 2530) link_ALPHA1-3 : bond 0.00338 / 0.17 ( 4) link_ALPHA1-3 : angle 1.54395 / 0.80 ( 12) link_ALPHA1-6 : bond 0.00385 / 0.20 ( 4) link_ALPHA1-6 : angle 1.56213 / 0.78 ( 12) link_BETA1-4 : bond 0.00425 / 0.26 ( 11) link_BETA1-4 : angle 1.90578 / 1.20 ( 33) link_NAG-ASN : bond 0.00318 / 0.16 ( 10) link_NAG-ASN : angle 2.52063 / 1.76 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 296 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.9375 (mtt) cc_final: 0.9007 (mtt) REVERT: A 256 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8279 (ttp) REVERT: A 535 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.6951 (mpm) REVERT: B 224 GLN cc_start: 0.8671 (tp40) cc_final: 0.8410 (tp40) REVERT: C 49 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7282 (pp-130) REVERT: C 137 MET cc_start: 0.8980 (mmp) cc_final: 0.8754 (mmm) REVERT: C 138 MET cc_start: 0.9276 (mtt) cc_final: 0.8902 (mtt) REVERT: C 301 PHE cc_start: 0.7366 (t80) cc_final: 0.7113 (t80) REVERT: D 17 ASP cc_start: 0.8460 (m-30) cc_final: 0.8254 (m-30) REVERT: D 234 ILE cc_start: 0.9257 (mt) cc_final: 0.8954 (mp) REVERT: D 243 ASN cc_start: 0.8354 (t0) cc_final: 0.7667 (t0) REVERT: E 83 MET cc_start: 0.9273 (mmm) cc_final: 0.9030 (mmm) REVERT: E 430 TYR cc_start: 0.8225 (m-80) cc_final: 0.7847 (m-80) REVERT: F 425 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.7345 (ptp-170) REVERT: F 460 ASP cc_start: 0.7391 (p0) cc_final: 0.7126 (p0) REVERT: F 467 TYR cc_start: 0.8315 (m-80) cc_final: 0.8032 (m-80) REVERT: F 472 ASN cc_start: 0.7980 (t0) cc_final: 0.6967 (t0) REVERT: F 474 LYS cc_start: 0.8069 (mmtt) cc_final: 0.7499 (mmtp) REVERT: G 6 GLU cc_start: 0.7991 (pm20) cc_final: 0.7681 (pm20) REVERT: G 464 ASN cc_start: 0.8456 (m-40) cc_final: 0.8028 (m-40) REVERT: G 472 ASN cc_start: 0.8280 (t0) cc_final: 0.7475 (t0) REVERT: G 473 LEU cc_start: 0.8970 (mt) cc_final: 0.8669 (mm) outliers start: 46 outliers final: 16 residues processed: 318 average time/residue: 0.5272 time to fit residues: 187.0917 Evaluate side-chains 298 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 278 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 431 GLU Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 497 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 68 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 138 optimal weight: 0.0980 chunk 163 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 157 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN A 262 GLN A 275 GLN ** C 64 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 ASN F 504 GLN G 1 GLN G 504 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.113397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.073839 restraints weight = 102232.608| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.93 r_work: 0.2698 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9153 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16336 Z= 0.146 Angle : 0.576 8.079 22268 Z= 0.298 Chirality : 0.044 0.212 2535 Planarity : 0.004 0.039 2704 Dihedral : 7.921 115.347 2214 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.21 % Allowed : 16.24 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.20), residues: 1888 helix: 2.10 (0.22), residues: 575 sheet: 0.77 (0.22), residues: 535 loop : 1.01 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 50 TYR 0.022 0.001 TYR B 299 PHE 0.032 0.002 PHE E 330 TRP 0.010 0.001 TRP D 67 HIS 0.002 0.001 HIS E 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (16300) covalent geometry : angle 0.56708 / 0.30 (22167) SS BOND : bond 0.00227 / 0.15 ( 7) SS BOND : angle 0.54382 / 0.34 ( 14) hydrogen bonds : bond 0.03937 / 2.55 ( 808) hydrogen bonds : angle 4.61459 / 3.30 ( 2530) link_ALPHA1-3 : bond 0.00358 / 0.18 ( 4) link_ALPHA1-3 : angle 1.46006 / 0.77 ( 12) link_ALPHA1-6 : bond 0.00368 / 0.19 ( 4) link_ALPHA1-6 : angle 1.47787 / 0.75 ( 12) link_BETA1-4 : bond 0.00303 / 0.17 ( 11) link_BETA1-4 : angle 1.61150 / 1.04 ( 33) link_NAG-ASN : bond 0.00128 / 0.07 ( 10) link_NAG-ASN : angle 2.06669 / 1.48 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 292 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 91 MET cc_start: 0.9385 (mtt) cc_final: 0.9043 (mtt) REVERT: A 216 LYS cc_start: 0.8450 (mppt) cc_final: 0.8194 (mmtm) REVERT: A 261 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8876 (mp) REVERT: A 302 LEU cc_start: 0.9270 (mt) cc_final: 0.8670 (mp) REVERT: B 224 GLN cc_start: 0.8742 (tp40) cc_final: 0.8540 (tp40) REVERT: C 49 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7299 (pp-130) REVERT: C 137 MET cc_start: 0.8955 (mmp) cc_final: 0.8685 (mmm) REVERT: C 138 MET cc_start: 0.9220 (mtt) cc_final: 0.8834 (mtt) REVERT: C 301 PHE cc_start: 0.7220 (t80) cc_final: 0.6975 (t80) REVERT: D 17 ASP cc_start: 0.8484 (m-30) cc_final: 0.8252 (m-30) REVERT: D 234 ILE cc_start: 0.9288 (mt) cc_final: 0.8974 (mp) REVERT: D 243 ASN cc_start: 0.8381 (t0) cc_final: 0.7666 (t0) REVERT: E 83 MET cc_start: 0.9272 (mmm) cc_final: 0.9025 (mmm) REVERT: E 430 TYR cc_start: 0.8234 (m-80) cc_final: 0.7896 (m-80) REVERT: F 460 ASP cc_start: 0.7414 (p0) cc_final: 0.7092 (p0) REVERT: F 467 TYR cc_start: 0.8319 (m-80) cc_final: 0.8103 (m-80) REVERT: F 472 ASN cc_start: 0.8030 (t0) cc_final: 0.7113 (t0) REVERT: F 474 LYS cc_start: 0.8049 (mmtt) cc_final: 0.7669 (mmtp) REVERT: F 507 GLN cc_start: 0.7036 (tm-30) cc_final: 0.6769 (tm-30) REVERT: G 460 ASP cc_start: 0.7756 (p0) cc_final: 0.7355 (p0) REVERT: G 464 ASN cc_start: 0.8427 (m-40) cc_final: 0.8023 (m-40) REVERT: G 469 GLU cc_start: 0.7935 (mp0) cc_final: 0.7649 (mp0) REVERT: G 472 ASN cc_start: 0.8272 (t0) cc_final: 0.7778 (t0) REVERT: G 473 LEU cc_start: 0.8971 (mt) cc_final: 0.8543 (mm) REVERT: G 474 LYS cc_start: 0.8256 (mptt) cc_final: 0.7898 (mmmt) REVERT: G 486 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.8957 (tttm) outliers start: 36 outliers final: 8 residues processed: 308 average time/residue: 0.5767 time to fit residues: 197.9515 Evaluate side-chains 291 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 280 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain G residue 404 SER Chi-restraints excluded: chain G residue 431 GLU Chi-restraints excluded: chain G residue 486 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 3 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 GLN ** C 64 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN F 464 ASN ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 504 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.113634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.074513 restraints weight = 95831.413| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 4.06 r_work: 0.2690 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16336 Z= 0.135 Angle : 0.569 9.090 22268 Z= 0.293 Chirality : 0.043 0.200 2535 Planarity : 0.004 0.043 2704 Dihedral : 7.761 114.061 2213 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.97 % Allowed : 16.60 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.88 (0.20), residues: 1888 helix: 2.16 (0.21), residues: 575 sheet: 0.87 (0.23), residues: 529 loop : 1.01 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 50 TYR 0.022 0.001 TYR B 299 PHE 0.033 0.002 PHE E 330 TRP 0.011 0.001 TRP B 237 HIS 0.002 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (16300) covalent geometry : angle 0.56036 / 0.29 (22167) SS BOND : bond 0.00211 / 0.15 ( 7) SS BOND : angle 0.62215 / 0.40 ( 14) hydrogen bonds : bond 0.03753 / 2.42 ( 808) hydrogen bonds : angle 4.47591 / 3.20 ( 2530) link_ALPHA1-3 : bond 0.00371 / 0.19 ( 4) link_ALPHA1-3 : angle 1.43359 / 0.76 ( 12) link_ALPHA1-6 : bond 0.00364 / 0.19 ( 4) link_ALPHA1-6 : angle 1.47127 / 0.75 ( 12) link_BETA1-4 : bond 0.00270 / 0.16 ( 11) link_BETA1-4 : angle 1.56777 / 1.01 ( 33) link_NAG-ASN : bond 0.00118 / 0.06 ( 10) link_NAG-ASN : angle 1.92830 / 1.39 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 297 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8462 (mppt) cc_final: 0.8175 (mmtm) REVERT: A 261 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8806 (mt) REVERT: A 302 LEU cc_start: 0.9251 (mt) cc_final: 0.8661 (mp) REVERT: B 224 GLN cc_start: 0.8694 (tp40) cc_final: 0.8444 (tp40) REVERT: C 49 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7360 (pp-130) REVERT: C 137 MET cc_start: 0.8964 (mmp) cc_final: 0.8677 (mmm) REVERT: C 138 MET cc_start: 0.9220 (mtt) cc_final: 0.8837 (mtt) REVERT: C 301 PHE cc_start: 0.7214 (t80) cc_final: 0.6978 (t80) REVERT: D 17 ASP cc_start: 0.8498 (m-30) cc_final: 0.8180 (m-30) REVERT: D 190 GLU cc_start: 0.8946 (tt0) cc_final: 0.8650 (tt0) REVERT: D 234 ILE cc_start: 0.9271 (mt) cc_final: 0.8941 (mp) REVERT: D 243 ASN cc_start: 0.8345 (t0) cc_final: 0.7592 (t0) REVERT: D 267 HIS cc_start: 0.8078 (t70) cc_final: 0.7840 (t-90) REVERT: E 228 PHE cc_start: 0.8049 (m-80) cc_final: 0.7769 (m-80) REVERT: E 233 GLN cc_start: 0.8622 (tt0) cc_final: 0.8167 (tp40) REVERT: E 430 TYR cc_start: 0.8244 (m-80) cc_final: 0.7949 (m-80) REVERT: F 3 GLN cc_start: 0.8095 (mp10) cc_final: 0.7732 (mp10) REVERT: F 460 ASP cc_start: 0.7402 (p0) cc_final: 0.7114 (p0) REVERT: F 467 TYR cc_start: 0.8350 (m-80) cc_final: 0.8111 (m-80) REVERT: F 472 ASN cc_start: 0.8101 (t0) cc_final: 0.7705 (t0) REVERT: F 474 LYS cc_start: 0.8107 (mmtt) cc_final: 0.7736 (mmmt) REVERT: G 460 ASP cc_start: 0.7795 (p0) cc_final: 0.7572 (p0) REVERT: G 464 ASN cc_start: 0.8458 (m-40) cc_final: 0.8099 (m-40) REVERT: G 469 GLU cc_start: 0.7828 (mp0) cc_final: 0.7582 (mp0) REVERT: G 472 ASN cc_start: 0.8306 (t0) cc_final: 0.7809 (t0) REVERT: G 473 LEU cc_start: 0.8987 (mt) cc_final: 0.8569 (mm) REVERT: G 474 LYS cc_start: 0.8302 (mptt) cc_final: 0.7963 (mmmt) outliers start: 32 outliers final: 9 residues processed: 310 average time/residue: 0.5815 time to fit residues: 200.7748 Evaluate side-chains 291 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 280 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain G residue 404 SER Chi-restraints excluded: chain G residue 431 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 142 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 GLN ** C 64 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 ASN ** F 504 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 = 0.3559 r_free = 0.3559 target = 0.113115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.073339 restraints weight = 104957.194| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 4.22 r_work: 0.2667 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9151 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16336 Z= 0.157 Angle : 0.584 9.316 22268 Z= 0.300 Chirality : 0.044 0.251 2535 Planarity : 0.004 0.038 2704 Dihedral : 7.741 113.820 2213 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.97 % Allowed : 16.42 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.87 (0.20), residues: 1888 helix: 2.17 (0.21), residues: 575 sheet: 0.86 (0.23), residues: 526 loop : 0.99 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 406 TYR 0.023 0.001 TYR D 299 PHE 0.034 0.002 PHE E 330 TRP 0.014 0.001 TRP B 237 HIS 0.003 0.001 HIS F 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (16300) covalent geometry : angle 0.57376 / 0.30 (22167) SS BOND : bond 0.00230 / 0.16 ( 7) SS BOND : angle 0.68374 / 0.42 ( 14) hydrogen bonds : bond 0.03790 / 2.46 ( 808) hydrogen bonds : angle 4.47524 / 3.19 ( 2530) link_ALPHA1-3 : bond 0.00343 / 0.17 ( 4) link_ALPHA1-3 : angle 1.46722 / 0.78 ( 12) link_ALPHA1-6 : bond 0.00374 / 0.19 ( 4) link_ALPHA1-6 : angle 1.47661 / 0.75 ( 12) link_BETA1-4 : bond 0.00306 / 0.18 ( 11) link_BETA1-4 : angle 1.65533 / 1.07 ( 33) link_NAG-ASN : bond 0.00212 / 0.11 ( 10) link_NAG-ASN : angle 2.15957 / 1.58 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 287 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8517 (mppt) cc_final: 0.8198 (mmtm) REVERT: A 261 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8795 (mt) REVERT: A 302 LEU cc_start: 0.9263 (mt) cc_final: 0.8680 (mp) REVERT: B 224 GLN cc_start: 0.8717 (tp40) cc_final: 0.8514 (tp40) REVERT: C 49 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7373 (pp-130) REVERT: C 137 MET cc_start: 0.8988 (mmp) cc_final: 0.8729 (mmm) REVERT: C 138 MET cc_start: 0.9229 (mtt) cc_final: 0.8838 (mtt) REVERT: C 301 PHE cc_start: 0.7214 (t80) cc_final: 0.6987 (t80) REVERT: D 17 ASP cc_start: 0.8491 (m-30) cc_final: 0.8122 (m-30) REVERT: D 243 ASN cc_start: 0.8316 (t0) cc_final: 0.7576 (t0) REVERT: D 267 HIS cc_start: 0.8132 (t70) cc_final: 0.7841 (t-90) REVERT: E 83 MET cc_start: 0.9334 (mmm) cc_final: 0.9118 (mmm) REVERT: E 228 PHE cc_start: 0.8134 (m-80) cc_final: 0.7742 (m-80) REVERT: E 233 GLN cc_start: 0.8706 (tt0) cc_final: 0.8191 (tp40) REVERT: E 430 TYR cc_start: 0.8257 (m-80) cc_final: 0.7938 (m-80) REVERT: F 460 ASP cc_start: 0.7457 (p0) cc_final: 0.7033 (p0) REVERT: F 467 TYR cc_start: 0.8377 (m-80) cc_final: 0.8078 (m-80) REVERT: F 472 ASN cc_start: 0.8212 (t0) cc_final: 0.7866 (t0) REVERT: F 474 LYS cc_start: 0.8033 (mmtt) cc_final: 0.7597 (mmmm) REVERT: F 477 ASP cc_start: 0.7117 (m-30) cc_final: 0.6892 (m-30) REVERT: G 460 ASP cc_start: 0.7813 (p0) cc_final: 0.7595 (p0) REVERT: G 464 ASN cc_start: 0.8524 (m-40) cc_final: 0.8178 (m-40) REVERT: G 472 ASN cc_start: 0.8365 (t0) cc_final: 0.7840 (t0) REVERT: G 473 LEU cc_start: 0.9021 (mt) cc_final: 0.8563 (mm) REVERT: G 474 LYS cc_start: 0.8330 (mptt) cc_final: 0.7980 (mmmt) outliers start: 32 outliers final: 12 residues processed: 298 average time/residue: 0.5760 time to fit residues: 191.7089 Evaluate side-chains 290 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 276 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain G residue 404 SER Chi-restraints excluded: chain G residue 463 LYS Chi-restraints excluded: chain G residue 509 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 141 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 GLN ** C 64 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN F 464 ASN ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.111713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.072439 restraints weight = 89913.124| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.94 r_work: 0.2653 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9161 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16336 Z= 0.195 Angle : 0.619 9.467 22268 Z= 0.318 Chirality : 0.045 0.278 2535 Planarity : 0.004 0.041 2704 Dihedral : 7.840 113.314 2213 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.61 % Allowed : 17.07 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.82 (0.20), residues: 1888 helix: 2.13 (0.21), residues: 572 sheet: 0.86 (0.23), residues: 526 loop : 0.93 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 406 TYR 0.025 0.002 TYR D 299 PHE 0.034 0.002 PHE E 330 TRP 0.009 0.001 TRP B 237 HIS 0.004 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (16300) covalent geometry : angle 0.60804 / 0.32 (22167) SS BOND : bond 0.00268 / 0.19 ( 7) SS BOND : angle 0.87057 / 0.51 ( 14) hydrogen bonds : bond 0.03973 / 2.57 ( 808) hydrogen bonds : angle 4.57744 / 3.27 ( 2530) link_ALPHA1-3 : bond 0.00304 / 0.16 ( 4) link_ALPHA1-3 : angle 1.50280 / 0.79 ( 12) link_ALPHA1-6 : bond 0.00365 / 0.19 ( 4) link_ALPHA1-6 : angle 1.51678 / 0.77 ( 12) link_BETA1-4 : bond 0.00341 / 0.21 ( 11) link_BETA1-4 : angle 1.80006 / 1.16 ( 33) link_NAG-ASN : bond 0.00288 / 0.16 ( 10) link_NAG-ASN : angle 2.33026 / 1.67 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 293 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8573 (mppt) cc_final: 0.8239 (mmtm) REVERT: A 261 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8778 (mt) REVERT: A 302 LEU cc_start: 0.9266 (mt) cc_final: 0.8678 (mp) REVERT: C 49 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7326 (pp-130) REVERT: C 137 MET cc_start: 0.8978 (mmp) cc_final: 0.8700 (mmm) REVERT: D 17 ASP cc_start: 0.8507 (m-30) cc_final: 0.8141 (m-30) REVERT: D 243 ASN cc_start: 0.8339 (t0) cc_final: 0.7621 (t0) REVERT: D 267 HIS cc_start: 0.8077 (t70) cc_final: 0.7805 (t-90) REVERT: E 430 TYR cc_start: 0.8246 (m-80) cc_final: 0.7943 (m-80) REVERT: F 3 GLN cc_start: 0.8196 (mp10) cc_final: 0.7789 (mp10) REVERT: F 460 ASP cc_start: 0.7575 (p0) cc_final: 0.7307 (p0) REVERT: F 467 TYR cc_start: 0.8435 (m-80) cc_final: 0.8121 (m-80) REVERT: F 472 ASN cc_start: 0.8270 (t0) cc_final: 0.7954 (t0) REVERT: F 474 LYS cc_start: 0.8039 (mmtt) cc_final: 0.7547 (mmmt) REVERT: G 460 ASP cc_start: 0.7813 (p0) cc_final: 0.7606 (p0) REVERT: G 464 ASN cc_start: 0.8611 (m-40) cc_final: 0.8299 (m110) REVERT: G 472 ASN cc_start: 0.8441 (t0) cc_final: 0.7960 (t0) REVERT: G 473 LEU cc_start: 0.9050 (mt) cc_final: 0.8633 (mm) REVERT: G 474 LYS cc_start: 0.8376 (mptt) cc_final: 0.8011 (mmmt) outliers start: 26 outliers final: 10 residues processed: 302 average time/residue: 0.5377 time to fit residues: 181.8063 Evaluate side-chains 294 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 282 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain G residue 404 SER Chi-restraints excluded: chain G residue 463 LYS Chi-restraints excluded: chain G residue 509 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 GLN ** C 64 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 414 HIS F 464 ASN G 3 GLN ** G 504 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 = 0.3541 r_free = 0.3541 target = 0.111922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.072444 restraints weight = 82348.995| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.64 r_work: 0.2669 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9153 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16336 Z= 0.187 Angle : 0.620 9.097 22268 Z= 0.319 Chirality : 0.045 0.351 2535 Planarity : 0.004 0.050 2704 Dihedral : 7.819 113.477 2213 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.55 % Allowed : 17.85 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.20), residues: 1888 helix: 2.03 (0.21), residues: 572 sheet: 0.94 (0.23), residues: 511 loop : 0.83 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 50 TYR 0.025 0.002 TYR D 299 PHE 0.034 0.002 PHE E 330 TRP 0.010 0.001 TRP B 237 HIS 0.004 0.001 HIS F 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (16300) covalent geometry : angle 0.60984 / 0.32 (22167) SS BOND : bond 0.00233 / 0.16 ( 7) SS BOND : angle 0.72258 / 0.41 ( 14) hydrogen bonds : bond 0.03909 / 2.52 ( 808) hydrogen bonds : angle 4.55611 / 3.25 ( 2530) link_ALPHA1-3 : bond 0.00306 / 0.16 ( 4) link_ALPHA1-3 : angle 1.47922 / 0.78 ( 12) link_ALPHA1-6 : bond 0.00344 / 0.18 ( 4) link_ALPHA1-6 : angle 1.51420 / 0.77 ( 12) link_BETA1-4 : bond 0.00343 / 0.21 ( 11) link_BETA1-4 : angle 1.74676 / 1.13 ( 33) link_NAG-ASN : bond 0.00249 / 0.14 ( 10) link_NAG-ASN : angle 2.29458 / 1.65 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 291 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8777 (mt) REVERT: A 302 LEU cc_start: 0.9273 (mt) cc_final: 0.8681 (mp) REVERT: B 103 LYS cc_start: 0.9158 (ttpm) cc_final: 0.8940 (ttpp) REVERT: C 49 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7291 (pp-130) REVERT: C 137 MET cc_start: 0.8939 (mmp) cc_final: 0.8673 (mmm) REVERT: D 17 ASP cc_start: 0.8474 (m-30) cc_final: 0.8122 (m-30) REVERT: D 190 GLU cc_start: 0.8888 (tt0) cc_final: 0.8582 (tt0) REVERT: D 243 ASN cc_start: 0.8341 (t0) cc_final: 0.7646 (t0) REVERT: D 267 HIS cc_start: 0.8028 (t70) cc_final: 0.7758 (t-90) REVERT: E 233 GLN cc_start: 0.8598 (tt0) cc_final: 0.8135 (tp40) REVERT: E 430 TYR cc_start: 0.8253 (m-80) cc_final: 0.7948 (m-80) REVERT: F 460 ASP cc_start: 0.7530 (p0) cc_final: 0.7316 (p0) REVERT: F 467 TYR cc_start: 0.8423 (m-80) cc_final: 0.8113 (m-80) REVERT: F 472 ASN cc_start: 0.8288 (t0) cc_final: 0.8015 (t0) REVERT: F 474 LYS cc_start: 0.8013 (mmtt) cc_final: 0.7617 (mmmt) REVERT: G 460 ASP cc_start: 0.7801 (p0) cc_final: 0.7565 (p0) REVERT: G 464 ASN cc_start: 0.8655 (m-40) cc_final: 0.8353 (m110) REVERT: G 472 ASN cc_start: 0.8433 (t0) cc_final: 0.7557 (t0) REVERT: G 473 LEU cc_start: 0.9077 (mt) cc_final: 0.8715 (mm) REVERT: G 474 LYS cc_start: 0.8374 (mptt) cc_final: 0.7918 (mptp) outliers start: 25 outliers final: 13 residues processed: 302 average time/residue: 0.5428 time to fit residues: 183.1035 Evaluate side-chains 296 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 281 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain G residue 1 GLN Chi-restraints excluded: chain G residue 404 SER Chi-restraints excluded: chain G residue 497 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 112 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 163 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN A 275 GLN A 341 ASN ** C 64 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 414 HIS F 464 ASN ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 504 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.113184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.074012 restraints weight = 94569.446| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 4.02 r_work: 0.2702 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9137 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16336 Z= 0.138 Angle : 0.602 11.378 22268 Z= 0.308 Chirality : 0.044 0.421 2535 Planarity : 0.004 0.053 2704 Dihedral : 7.686 113.894 2213 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.13 % Allowed : 18.21 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.20), residues: 1888 helix: 1.96 (0.21), residues: 575 sheet: 0.93 (0.23), residues: 520 loop : 0.90 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 50 TYR 0.022 0.001 TYR B 299 PHE 0.034 0.002 PHE E 330 TRP 0.011 0.001 TRP D 67 HIS 0.003 0.001 HIS F 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (16300) covalent geometry : angle 0.59366 / 0.31 (22167) SS BOND : bond 0.00163 / 0.11 ( 7) SS BOND : angle 0.46709 / 0.28 ( 14) hydrogen bonds : bond 0.03673 / 2.37 ( 808) hydrogen bonds : angle 4.45744 / 3.18 ( 2530) link_ALPHA1-3 : bond 0.00362 / 0.18 ( 4) link_ALPHA1-3 : angle 1.42672 / 0.76 ( 12) link_ALPHA1-6 : bond 0.00338 / 0.17 ( 4) link_ALPHA1-6 : angle 1.49386 / 0.76 ( 12) link_BETA1-4 : bond 0.00287 / 0.16 ( 11) link_BETA1-4 : angle 1.55171 / 1.01 ( 33) link_NAG-ASN : bond 0.00194 / 0.11 ( 10) link_NAG-ASN : angle 2.01478 / 1.48 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 299 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 49 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7348 (pp-130) REVERT: C 137 MET cc_start: 0.8943 (mmp) cc_final: 0.8673 (mmm) REVERT: D 17 ASP cc_start: 0.8484 (m-30) cc_final: 0.8124 (m-30) REVERT: D 190 GLU cc_start: 0.8908 (tt0) cc_final: 0.8522 (tt0) REVERT: D 243 ASN cc_start: 0.8315 (t0) cc_final: 0.7599 (t0) REVERT: D 267 HIS cc_start: 0.8016 (t70) cc_final: 0.7742 (t-90) REVERT: D 425 ARG cc_start: 0.6178 (mpt180) cc_final: 0.5766 (mtm-85) REVERT: E 213 GLN cc_start: 0.8915 (tt0) cc_final: 0.8515 (tt0) REVERT: E 228 PHE cc_start: 0.8231 (m-80) cc_final: 0.7910 (m-80) REVERT: E 233 GLN cc_start: 0.8551 (tt0) cc_final: 0.8080 (tp40) REVERT: E 430 TYR cc_start: 0.8241 (m-80) cc_final: 0.7939 (m-80) REVERT: F 460 ASP cc_start: 0.7565 (p0) cc_final: 0.7276 (p0) REVERT: F 467 TYR cc_start: 0.8421 (m-80) cc_final: 0.8119 (m-80) REVERT: F 472 ASN cc_start: 0.8248 (t0) cc_final: 0.7935 (t0) REVERT: F 474 LYS cc_start: 0.7922 (mmtt) cc_final: 0.7411 (mttm) REVERT: G 406 ARG cc_start: 0.7762 (tpt170) cc_final: 0.7535 (tpt170) REVERT: G 460 ASP cc_start: 0.7699 (p0) cc_final: 0.7472 (p0) REVERT: G 464 ASN cc_start: 0.8636 (m-40) cc_final: 0.8277 (m-40) REVERT: G 472 ASN cc_start: 0.8460 (t0) cc_final: 0.7579 (t0) REVERT: G 473 LEU cc_start: 0.9084 (mt) cc_final: 0.8749 (mm) REVERT: G 474 LYS cc_start: 0.8381 (mptt) cc_final: 0.7919 (mptp) outliers start: 18 outliers final: 11 residues processed: 306 average time/residue: 0.5313 time to fit residues: 181.5607 Evaluate side-chains 299 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 287 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain G residue 404 SER Chi-restraints excluded: chain G residue 469 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 161 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 chunk 113 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN A 262 GLN A 275 GLN A 341 ASN ** C 64 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN F 414 HIS F 464 ASN ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.114331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.075348 restraints weight = 101556.328| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 4.12 r_work: 0.2721 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9123 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16336 Z= 0.120 Angle : 0.603 10.056 22268 Z= 0.306 Chirality : 0.043 0.268 2535 Planarity : 0.004 0.054 2704 Dihedral : 7.582 113.911 2213 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.90 % Allowed : 19.16 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.20), residues: 1888 helix: 1.96 (0.21), residues: 575 sheet: 1.03 (0.23), residues: 520 loop : 0.91 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 50 TYR 0.021 0.001 TYR C 299 PHE 0.035 0.001 PHE E 330 TRP 0.013 0.001 TRP D 67 HIS 0.004 0.001 HIS F 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (16300) covalent geometry : angle 0.59612 / 0.30 (22167) SS BOND : bond 0.00131 / 0.08 ( 7) SS BOND : angle 0.40367 / 0.23 ( 14) hydrogen bonds : bond 0.03468 / 2.25 ( 808) hydrogen bonds : angle 4.35810 / 3.12 ( 2530) link_ALPHA1-3 : bond 0.00420 / 0.21 ( 4) link_ALPHA1-3 : angle 1.42909 / 0.77 ( 12) link_ALPHA1-6 : bond 0.00360 / 0.18 ( 4) link_ALPHA1-6 : angle 1.47966 / 0.76 ( 12) link_BETA1-4 : bond 0.00290 / 0.17 ( 11) link_BETA1-4 : angle 1.46867 / 0.97 ( 33) link_NAG-ASN : bond 0.00203 / 0.11 ( 10) link_NAG-ASN : angle 1.84503 / 1.36 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 307 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 MET cc_start: 0.8417 (ptm) cc_final: 0.8008 (pp-130) REVERT: C 49 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7397 (pp-130) REVERT: C 137 MET cc_start: 0.8942 (mmp) cc_final: 0.8667 (mmm) REVERT: C 444 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8237 (mt) REVERT: D 243 ASN cc_start: 0.8273 (t0) cc_final: 0.7575 (t0) REVERT: D 267 HIS cc_start: 0.8004 (t70) cc_final: 0.7726 (t-90) REVERT: E 213 GLN cc_start: 0.8886 (tt0) cc_final: 0.8490 (tt0) REVERT: E 228 PHE cc_start: 0.8149 (m-80) cc_final: 0.7846 (m-80) REVERT: E 233 GLN cc_start: 0.8542 (tt0) cc_final: 0.8072 (tp40) REVERT: E 430 TYR cc_start: 0.8296 (m-80) cc_final: 0.7984 (m-80) REVERT: F 460 ASP cc_start: 0.7587 (p0) cc_final: 0.7282 (p0) REVERT: F 467 TYR cc_start: 0.8414 (m-80) cc_final: 0.8171 (m-80) REVERT: F 472 ASN cc_start: 0.8251 (t0) cc_final: 0.7955 (t0) REVERT: F 474 LYS cc_start: 0.7943 (mmtt) cc_final: 0.7478 (mttm) REVERT: G 6 GLU cc_start: 0.8108 (pm20) cc_final: 0.7877 (pm20) REVERT: G 460 ASP cc_start: 0.7607 (p0) cc_final: 0.7406 (p0) REVERT: G 464 ASN cc_start: 0.8628 (m-40) cc_final: 0.8274 (m-40) REVERT: G 472 ASN cc_start: 0.8469 (t0) cc_final: 0.8048 (t0) REVERT: G 473 LEU cc_start: 0.9058 (mt) cc_final: 0.8781 (mt) REVERT: G 474 LYS cc_start: 0.8355 (mptt) cc_final: 0.7981 (mmmt) outliers start: 14 outliers final: 7 residues processed: 311 average time/residue: 0.5236 time to fit residues: 182.4826 Evaluate side-chains 302 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 293 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain G residue 404 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 141 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 132 optimal weight: 0.1980 chunk 77 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 GLN A 341 ASN ** C 64 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 414 HIS F 464 ASN ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.113824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.074585 restraints weight = 97308.990| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.90 r_work: 0.2733 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16336 Z= 0.127 Angle : 0.606 10.911 22268 Z= 0.306 Chirality : 0.044 0.350 2535 Planarity : 0.004 0.045 2704 Dihedral : 7.580 113.510 2213 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.84 % Allowed : 19.94 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.82 (0.20), residues: 1888 helix: 1.96 (0.21), residues: 575 sheet: 1.07 (0.23), residues: 520 loop : 0.91 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 50 TYR 0.021 0.001 TYR D 299 PHE 0.034 0.001 PHE E 330 TRP 0.017 0.001 TRP G 440 HIS 0.004 0.001 HIS F 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (16300) covalent geometry : angle 0.59917 / 0.31 (22167) SS BOND : bond 0.00161 / 0.11 ( 7) SS BOND : angle 0.47477 / 0.28 ( 14) hydrogen bonds : bond 0.03491 / 2.27 ( 808) hydrogen bonds : angle 4.35743 / 3.10 ( 2530) link_ALPHA1-3 : bond 0.00362 / 0.18 ( 4) link_ALPHA1-3 : angle 1.42291 / 0.76 ( 12) link_ALPHA1-6 : bond 0.00351 / 0.18 ( 4) link_ALPHA1-6 : angle 1.46170 / 0.75 ( 12) link_BETA1-4 : bond 0.00305 / 0.18 ( 11) link_BETA1-4 : angle 1.50910 / 0.99 ( 33) link_NAG-ASN : bond 0.00189 / 0.10 ( 10) link_NAG-ASN : angle 1.84205 / 1.35 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6996.57 seconds wall clock time: 119 minutes 52.38 seconds (7192.38 seconds total)