Starting phenix.real_space_refine on Sat Sep 28 02:01:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smm_25202/09_2024/7smm_25202.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smm_25202/09_2024/7smm_25202.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smm_25202/09_2024/7smm_25202.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smm_25202/09_2024/7smm_25202.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smm_25202/09_2024/7smm_25202.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smm_25202/09_2024/7smm_25202.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 86 5.16 5 C 11267 2.51 5 N 2659 2.21 5 O 3236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17256 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3204 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 374} Chain breaks: 1 Chain: "B" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3451 Classifications: {'peptide': 425} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 397} Chain breaks: 1 Chain: "C" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3294 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 382} Chain breaks: 1 Chain: "D" Number of atoms: 3204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3204 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 374} Chain breaks: 1 Chain: "E" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3315 Classifications: {'peptide': 409} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 387} Chain breaks: 1 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'CLR': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 108 Unusual residues: {'DD9': 1, 'NAG': 2, 'POV': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'CLR': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'CLR': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 124 Unusual residues: {'NAG': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Residues with excluded nonbonded symmetry interactions: 11 residue: pdb=" N POV A 501 " occ=0.75 ... (44 atoms not shown) pdb="C314 POV A 501 " occ=0.75 residue: pdb=" C1 CLR A 502 " occ=0.80 ... (26 atoms not shown) pdb=" O1 CLR A 502 " occ=0.80 residue: pdb=" N POV B 603 " occ=0.75 ... (33 atoms not shown) pdb="C311 POV B 603 " occ=0.75 residue: pdb=" N POV B 604 " occ=0.75 ... (35 atoms not shown) pdb="C311 POV B 604 " occ=0.75 residue: pdb=" N POV C 501 " occ=0.75 ... (30 atoms not shown) pdb=" P POV C 501 " occ=0.75 residue: pdb=" C1 CLR C 502 " occ=0.89 ... (26 atoms not shown) pdb=" O1 CLR C 502 " occ=0.89 residue: pdb=" C1 CLR D 501 " occ=0.75 ... (26 atoms not shown) pdb=" O1 CLR D 501 " occ=0.75 residue: pdb=" N POV D 502 " occ=0.75 ... (35 atoms not shown) pdb="C310 POV D 502 " occ=0.75 residue: pdb=" N POV E 502 " occ=0.75 ... (38 atoms not shown) pdb="C215 POV E 502 " occ=0.75 residue: pdb=" N POV E 503 " occ=0.75 ... (33 atoms not shown) pdb=" P POV E 503 " occ=0.75 residue: pdb=" N POV E 504 " occ=0.75 ... (33 atoms not shown) pdb="C311 POV E 504 " occ=0.75 Time building chain proxies: 9.30, per 1000 atoms: 0.54 Number of scatterers: 17256 At special positions: 0 Unit cell: (101.593, 165.757, 114.426, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 86 16.00 P 8 15.00 O 3236 8.00 N 2659 7.00 C 11267 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 193 " distance=2.05 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.04 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.04 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.05 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 7 " " MAN F 4 " - " MAN F 5 " " BMA I 3 " - " MAN I 7 " " MAN I 4 " - " MAN I 5 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 6 " " BMA I 3 " - " MAN I 4 " " MAN I 4 " - " MAN I 6 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG B 601 " - " ASN B 70 " " NAG B 602 " - " ASN B 208 " " NAG E 501 " - " ASN E 68 " " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 143 " " NAG H 1 " - " ASN C 141 " " NAG I 1 " - " ASN D 141 " " NAG J 1 " - " ASN E 141 " Time building additional restraints: 4.95 Conformation dependent library (CDL) restraints added in 2.1 seconds 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3920 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 43.3% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 63 through 66 removed outlier: 3.764A pdb=" N ARG A 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 68 through 73 removed outlier: 4.095A pdb=" N GLY A 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 212 through 218 Processing helix chain 'A' and resid 218 through 230 removed outlier: 3.879A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 241 through 264 removed outlier: 3.892A pdb=" N LEU A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 317 Processing helix chain 'A' and resid 319 through 324 removed outlier: 3.743A pdb=" N MET A 324 " --> pdb=" O PRO A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 433 removed outlier: 4.340A pdb=" N GLY A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 226 through 232 Processing helix chain 'B' and resid 232 through 242 removed outlier: 3.504A pdb=" N CYS B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 removed outlier: 4.043A pdb=" N TYR B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 276 removed outlier: 3.829A pdb=" N GLN B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 314 Processing helix chain 'B' and resid 323 through 332 Processing helix chain 'B' and resid 332 through 338 removed outlier: 3.583A pdb=" N ARG B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 478 Proline residue: B 463 - end of helix Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 68 through 73 removed outlier: 4.078A pdb=" N GLU C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.729A pdb=" N VAL C 85 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 180 removed outlier: 4.055A pdb=" N PHE C 180 " --> pdb=" O LYS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 238 Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 247 through 268 removed outlier: 4.425A pdb=" N ASP C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 306 Processing helix chain 'C' and resid 315 through 323 Processing helix chain 'C' and resid 325 through 331 removed outlier: 3.940A pdb=" N PHE C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 460 Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 63 through 66 removed outlier: 3.524A pdb=" N ARG D 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 66' Processing helix chain 'D' and resid 68 through 73 removed outlier: 4.241A pdb=" N GLY D 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 212 through 218 Processing helix chain 'D' and resid 218 through 232 Processing helix chain 'D' and resid 233 through 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' Processing helix chain 'D' and resid 241 through 264 Processing helix chain 'D' and resid 272 through 300 Processing helix chain 'D' and resid 309 through 317 Processing helix chain 'D' and resid 319 through 324 removed outlier: 3.571A pdb=" N MET D 324 " --> pdb=" O PRO D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 433 removed outlier: 3.770A pdb=" N PHE D 426 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY D 428 " --> pdb=" O SER D 424 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ARG D 429 " --> pdb=" O VAL D 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 removed outlier: 3.938A pdb=" N ARG E 6 " --> pdb=" O ASN E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 removed outlier: 4.169A pdb=" N GLU E 73 " --> pdb=" O SER E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 219 through 226 Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 236 through 243 removed outlier: 3.537A pdb=" N VAL E 240 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR E 241 " --> pdb=" O VAL E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 271 removed outlier: 3.885A pdb=" N GLN E 271 " --> pdb=" O PHE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 309 Processing helix chain 'E' and resid 318 through 327 Processing helix chain 'E' and resid 411 through 470 removed outlier: 3.672A pdb=" N GLY E 470 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.231A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.231A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 49 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL A 43 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLU A 51 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG A 55 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU A 37 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ARG A 57 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU A 35 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLN A 59 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N VAL A 33 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N ILE A 61 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILE A 31 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL A 29 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N SER A 159 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE A 31 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.634A pdb=" N CYS A 142 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR A 196 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TYR A 190 " --> pdb=" O THR A 196 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N MET A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 82 removed outlier: 4.747A pdb=" N GLY B 116 " --> pdb=" O ASP B 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 82 removed outlier: 4.747A pdb=" N GLY B 116 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR B 51 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N SER B 44 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN B 55 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR B 63 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN B 32 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 93 through 94 removed outlier: 6.799A pdb=" N ILE B 220 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 94 Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 80 removed outlier: 3.876A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 77 through 80 removed outlier: 3.876A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLU C 49 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE C 42 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR C 51 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASN C 53 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR C 61 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THR C 30 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C 161 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N LEU C 35 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA C 161 " --> pdb=" O VAL C 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.258A pdb=" N SER C 148 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLU C 205 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE C 212 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.258A pdb=" N SER C 148 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLU C 205 " --> pdb=" O SER C 148 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 81 removed outlier: 3.853A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 81 removed outlier: 3.853A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN D 53 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU D 40 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ARG D 55 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE D 38 " --> pdb=" O ARG D 55 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ARG D 57 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLN D 36 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLN D 59 " --> pdb=" O GLY D 34 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N GLY D 34 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N ILE D 61 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N THR D 32 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 90 through 92 removed outlier: 4.528A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR D 196 " --> pdb=" O TYR D 190 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TYR D 190 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN D 208 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N MET D 178 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.956A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.956A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ALA E 49 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER E 42 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU E 40 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASN E 61 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASP E 30 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE E 29 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLN E 159 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL E 31 " --> pdb=" O GLN E 159 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.361A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.361A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 162 through 163 946 hydrogen bonds defined for protein. 2739 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: 5.55 Time building geometry restraints manager: 5.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2668 1.32 - 1.45: 4882 1.45 - 1.59: 9928 1.59 - 1.72: 16 1.72 - 1.86: 140 Bond restraints: 17634 Sorted by residual: bond pdb=" C VAL B 93 " pdb=" N LEU B 94 " ideal model delta sigma weight residual 1.331 1.285 0.046 1.42e-02 4.96e+03 1.04e+01 bond pdb=" N POV E 503 " pdb=" C12 POV E 503 " ideal model delta sigma weight residual 1.508 1.450 0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" N POV E 502 " pdb=" C12 POV E 502 " ideal model delta sigma weight residual 1.508 1.452 0.056 2.00e-02 2.50e+03 7.98e+00 bond pdb=" N POV E 504 " pdb=" C12 POV E 504 " ideal model delta sigma weight residual 1.508 1.452 0.056 2.00e-02 2.50e+03 7.97e+00 bond pdb=" N POV A 501 " pdb=" C12 POV A 501 " ideal model delta sigma weight residual 1.508 1.452 0.056 2.00e-02 2.50e+03 7.90e+00 ... (remaining 17629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 23570 2.51 - 5.03: 387 5.03 - 7.54: 49 7.54 - 10.05: 8 10.05 - 12.57: 16 Bond angle restraints: 24030 Sorted by residual: angle pdb=" O11 POV D 502 " pdb=" P POV D 502 " pdb=" O12 POV D 502 " ideal model delta sigma weight residual 97.67 110.24 -12.57 3.00e+00 1.11e-01 1.75e+01 angle pdb=" O11 POV C 501 " pdb=" P POV C 501 " pdb=" O12 POV C 501 " ideal model delta sigma weight residual 97.67 109.90 -12.23 3.00e+00 1.11e-01 1.66e+01 angle pdb=" O13 POV A 501 " pdb=" P POV A 501 " pdb=" O14 POV A 501 " ideal model delta sigma weight residual 121.11 109.18 11.93 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O11 POV B 604 " pdb=" P POV B 604 " pdb=" O12 POV B 604 " ideal model delta sigma weight residual 97.67 109.57 -11.90 3.00e+00 1.11e-01 1.57e+01 angle pdb=" O13 POV B 604 " pdb=" P POV B 604 " pdb=" O14 POV B 604 " ideal model delta sigma weight residual 121.11 109.32 11.79 3.00e+00 1.11e-01 1.54e+01 ... (remaining 24025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.58: 10638 31.58 - 63.16: 296 63.16 - 94.74: 56 94.74 - 126.32: 18 126.32 - 157.90: 4 Dihedral angle restraints: 11012 sinusoidal: 4991 harmonic: 6021 Sorted by residual: dihedral pdb=" CA CYS A 142 " pdb=" C CYS A 142 " pdb=" N THR A 143 " pdb=" CA THR A 143 " ideal model delta harmonic sigma weight residual -180.00 -151.42 -28.58 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA CYS A 192 " pdb=" C CYS A 192 " pdb=" N CYS A 193 " pdb=" CA CYS A 193 " ideal model delta harmonic sigma weight residual -180.00 -153.12 -26.88 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CB CYS B 130 " pdb=" SG CYS B 130 " pdb=" SG CYS B 144 " pdb=" CB CYS B 144 " ideal model delta sinusoidal sigma weight residual 93.00 48.05 44.95 1 1.00e+01 1.00e-02 2.81e+01 ... (remaining 11009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2394 0.060 - 0.119: 398 0.119 - 0.179: 36 0.179 - 0.238: 9 0.238 - 0.298: 5 Chirality restraints: 2842 Sorted by residual: chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 141 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 2839 not shown) Planarity restraints: 2903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 222 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C VAL C 222 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL C 222 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR C 223 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 234 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO B 235 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 235 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 235 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 221 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C ILE C 221 " 0.028 2.00e-02 2.50e+03 pdb=" O ILE C 221 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL C 222 " -0.009 2.00e-02 2.50e+03 ... (remaining 2900 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 203 2.66 - 3.22: 16068 3.22 - 3.78: 27171 3.78 - 4.34: 39043 4.34 - 4.90: 63404 Nonbonded interactions: 145889 Sorted by model distance: nonbonded pdb=" O MET D 324 " pdb=" NH2 ARG D 331 " model vdw 2.099 3.120 nonbonded pdb=" NH1 ARG E 187 " pdb=" OE1 GLN E 216 " model vdw 2.187 3.120 nonbonded pdb=" OD2 ASP B 140 " pdb=" NE2 GLN B 142 " model vdw 2.213 3.120 nonbonded pdb=" OD1 ASP E 113 " pdb=" OG SER E 115 " model vdw 2.233 3.040 nonbonded pdb=" O LEU E 40 " pdb=" ND2 ASN E 181 " model vdw 2.237 3.120 ... (remaining 145884 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 433) selection = (chain 'D' and resid 1 through 433) } ncs_group { reference = chain 'F' selection = chain 'I' } 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=0.75 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 38.560 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 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 : 0.006 0.058 17634 Z= 0.366 Angle : 0.776 12.568 24030 Z= 0.337 Chirality : 0.046 0.298 2842 Planarity : 0.003 0.044 2895 Dihedral : 16.089 157.898 7071 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.19), residues: 2010 helix: 2.72 (0.18), residues: 747 sheet: 0.26 (0.26), residues: 413 loop : -0.41 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 176 HIS 0.006 0.001 HIS B 60 PHE 0.012 0.001 PHE E 422 TYR 0.009 0.001 TYR D 277 ARG 0.004 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.967 Fit side-chains revert: symmetry clash REVERT: E 198 GLN cc_start: 0.7937 (mp-120) cc_final: 0.7604 (mp10) outliers start: 0 outliers final: 1 residues processed: 147 average time/residue: 1.2861 time to fit residues: 211.8706 Evaluate side-chains 117 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 156 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 ASN B 213 GLN B 328 GLN E 431 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17634 Z= 0.318 Angle : 0.568 6.637 24030 Z= 0.295 Chirality : 0.044 0.190 2842 Planarity : 0.004 0.046 2895 Dihedral : 13.912 152.149 3140 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.91 % Allowed : 4.97 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.19), residues: 2010 helix: 2.72 (0.18), residues: 752 sheet: 0.37 (0.25), residues: 408 loop : -0.32 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 187 HIS 0.004 0.001 HIS B 313 PHE 0.015 0.002 PHE D 256 TYR 0.011 0.001 TYR D 277 ARG 0.006 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.954 Fit side-chains revert: symmetry clash REVERT: B 58 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7485 (mmp) REVERT: B 186 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7338 (mm-30) outliers start: 17 outliers final: 2 residues processed: 133 average time/residue: 1.2687 time to fit residues: 190.0481 Evaluate side-chains 116 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain D residue 83 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 196 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 180 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 GLN D 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17634 Z= 0.220 Angle : 0.512 8.553 24030 Z= 0.265 Chirality : 0.043 0.218 2842 Planarity : 0.004 0.050 2895 Dihedral : 12.370 134.666 3138 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.12 % Allowed : 6.57 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.19), residues: 2010 helix: 2.97 (0.18), residues: 748 sheet: 0.44 (0.25), residues: 407 loop : -0.32 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 187 HIS 0.004 0.001 HIS B 313 PHE 0.012 0.001 PHE D 256 TYR 0.012 0.001 TYR D 277 ARG 0.003 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 1.900 Fit side-chains revert: symmetry clash REVERT: B 58 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7375 (mmp) REVERT: B 186 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7336 (mm-30) outliers start: 21 outliers final: 11 residues processed: 136 average time/residue: 1.2768 time to fit residues: 195.1643 Evaluate side-chains 126 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 480 HIS Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 132 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 182 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17634 Z= 0.221 Angle : 0.509 7.547 24030 Z= 0.262 Chirality : 0.043 0.208 2842 Planarity : 0.004 0.053 2895 Dihedral : 11.664 124.062 3138 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.17 % Allowed : 8.33 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.19), residues: 2010 helix: 3.07 (0.18), residues: 747 sheet: 0.48 (0.25), residues: 408 loop : -0.31 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 187 HIS 0.004 0.001 HIS B 313 PHE 0.012 0.001 PHE B 473 TYR 0.012 0.001 TYR D 277 ARG 0.011 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 1.892 Fit side-chains revert: symmetry clash REVERT: A 260 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8200 (mt) REVERT: A 278 MET cc_start: 0.7375 (ttt) cc_final: 0.6930 (ttt) REVERT: A 404 MET cc_start: 0.8303 (tmm) cc_final: 0.8090 (tmt) REVERT: B 58 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7377 (mmp) REVERT: B 186 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7274 (mm-30) REVERT: B 214 ASP cc_start: 0.8558 (t70) cc_final: 0.8295 (t70) REVERT: C 165 LYS cc_start: 0.8542 (ptmt) cc_final: 0.7760 (tptt) REVERT: D 179 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8463 (mmpt) outliers start: 22 outliers final: 12 residues processed: 134 average time/residue: 1.4312 time to fit residues: 217.5687 Evaluate side-chains 131 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 480 HIS Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain E residue 287 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 chunk 48 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17634 Z= 0.170 Angle : 0.481 7.460 24030 Z= 0.247 Chirality : 0.042 0.228 2842 Planarity : 0.004 0.052 2895 Dihedral : 10.980 111.737 3138 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.60 % Allowed : 8.60 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 2010 helix: 3.19 (0.18), residues: 747 sheet: 0.48 (0.25), residues: 405 loop : -0.25 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 187 HIS 0.005 0.001 HIS B 313 PHE 0.011 0.001 PHE B 473 TYR 0.012 0.001 TYR D 277 ARG 0.008 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 1.873 Fit side-chains revert: symmetry clash REVERT: A 260 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8325 (mt) REVERT: B 214 ASP cc_start: 0.8504 (t70) cc_final: 0.8262 (t70) REVERT: E 438 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7306 (mm-30) outliers start: 30 outliers final: 13 residues processed: 141 average time/residue: 1.2146 time to fit residues: 193.2295 Evaluate side-chains 127 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 480 HIS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 438 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 0.7980 chunk 174 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 113 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 193 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17634 Z= 0.179 Angle : 0.481 8.735 24030 Z= 0.246 Chirality : 0.042 0.224 2842 Planarity : 0.004 0.050 2895 Dihedral : 10.725 105.043 3138 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.49 % Allowed : 9.13 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.19), residues: 2010 helix: 3.23 (0.18), residues: 747 sheet: 0.47 (0.25), residues: 405 loop : -0.24 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 187 HIS 0.005 0.001 HIS E 323 PHE 0.012 0.001 PHE B 473 TYR 0.009 0.001 TYR B 439 ARG 0.003 0.000 ARG B 336 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 1.834 Fit side-chains revert: symmetry clash REVERT: A 46 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8567 (t) REVERT: A 260 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8361 (mt) REVERT: A 278 MET cc_start: 0.7316 (ttt) cc_final: 0.6905 (ttt) REVERT: A 326 PHE cc_start: 0.7392 (m-10) cc_final: 0.6370 (p90) REVERT: B 186 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7244 (mt-10) REVERT: B 214 ASP cc_start: 0.8446 (t70) cc_final: 0.8211 (t70) REVERT: C 165 LYS cc_start: 0.8512 (ptmt) cc_final: 0.7740 (tptt) REVERT: E 438 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7312 (mm-30) outliers start: 28 outliers final: 16 residues processed: 138 average time/residue: 1.1695 time to fit residues: 183.2831 Evaluate side-chains 133 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 480 HIS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 438 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 162 optimal weight: 0.3980 chunk 108 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 88 optimal weight: 0.0970 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 HIS B 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 17634 Z= 0.167 Angle : 0.474 7.987 24030 Z= 0.243 Chirality : 0.042 0.225 2842 Planarity : 0.003 0.049 2895 Dihedral : 10.418 96.833 3138 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.28 % Allowed : 9.72 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.19), residues: 2010 helix: 3.26 (0.18), residues: 747 sheet: 0.49 (0.25), residues: 405 loop : -0.25 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 187 HIS 0.006 0.001 HIS E 323 PHE 0.011 0.001 PHE B 473 TYR 0.012 0.001 TYR D 277 ARG 0.003 0.000 ARG B 336 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8567 (t) REVERT: A 260 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8330 (mt) REVERT: A 278 MET cc_start: 0.7225 (ttt) cc_final: 0.6767 (ttt) REVERT: A 326 PHE cc_start: 0.7483 (m-10) cc_final: 0.6481 (p90) REVERT: B 186 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7246 (mt-10) REVERT: B 267 GLN cc_start: 0.8587 (mt0) cc_final: 0.8383 (mt0) REVERT: C 331 TRP cc_start: 0.7696 (m-10) cc_final: 0.7417 (m-90) REVERT: D 223 LEU cc_start: 0.8920 (mt) cc_final: 0.8661 (mm) REVERT: E 438 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7294 (mm-30) outliers start: 24 outliers final: 14 residues processed: 134 average time/residue: 1.1359 time to fit residues: 173.1376 Evaluate side-chains 128 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 438 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 151 optimal weight: 0.5980 chunk 175 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17634 Z= 0.184 Angle : 0.479 8.291 24030 Z= 0.245 Chirality : 0.042 0.222 2842 Planarity : 0.003 0.051 2895 Dihedral : 10.293 90.073 3138 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.39 % Allowed : 10.25 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.19), residues: 2010 helix: 3.27 (0.18), residues: 747 sheet: 0.52 (0.25), residues: 405 loop : -0.25 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 187 HIS 0.006 0.001 HIS E 323 PHE 0.012 0.001 PHE B 473 TYR 0.010 0.001 TYR B 439 ARG 0.003 0.000 ARG B 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 110 time to evaluate : 1.917 Fit side-chains REVERT: A 46 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8570 (t) REVERT: A 260 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8322 (mt) REVERT: A 278 MET cc_start: 0.7305 (ttt) cc_final: 0.6817 (ttt) REVERT: A 326 PHE cc_start: 0.7431 (m-10) cc_final: 0.6450 (p90) REVERT: B 186 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7252 (mt-10) REVERT: D 223 LEU cc_start: 0.8948 (mt) cc_final: 0.8674 (mm) REVERT: E 438 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7294 (mm-30) outliers start: 26 outliers final: 18 residues processed: 131 average time/residue: 1.1067 time to fit residues: 165.0146 Evaluate side-chains 131 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 438 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 0.0060 chunk 168 optimal weight: 0.9980 chunk 179 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 chunk 169 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17634 Z= 0.168 Angle : 0.471 8.033 24030 Z= 0.241 Chirality : 0.042 0.224 2842 Planarity : 0.003 0.052 2895 Dihedral : 10.019 86.209 3138 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.12 % Allowed : 10.57 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.19), residues: 2010 helix: 3.30 (0.18), residues: 747 sheet: 0.51 (0.25), residues: 406 loop : -0.23 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 60 HIS 0.006 0.001 HIS E 323 PHE 0.011 0.001 PHE B 473 TYR 0.010 0.001 TYR D 277 ARG 0.003 0.000 ARG B 336 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 1.899 Fit side-chains revert: symmetry clash REVERT: A 46 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8567 (t) REVERT: A 326 PHE cc_start: 0.7376 (m-10) cc_final: 0.6459 (p90) REVERT: B 186 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7249 (mt-10) REVERT: D 223 LEU cc_start: 0.8929 (mt) cc_final: 0.8669 (mm) REVERT: E 438 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7295 (mm-30) outliers start: 21 outliers final: 17 residues processed: 127 average time/residue: 1.1756 time to fit residues: 169.2238 Evaluate side-chains 129 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 438 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 199 optimal weight: 0.3980 chunk 183 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 97 optimal weight: 0.3980 chunk 126 optimal weight: 0.7980 chunk 169 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 17634 Z= 0.165 Angle : 0.471 7.783 24030 Z= 0.241 Chirality : 0.042 0.224 2842 Planarity : 0.003 0.052 2895 Dihedral : 9.754 83.462 3138 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.07 % Allowed : 10.62 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.19), residues: 2010 helix: 3.30 (0.18), residues: 748 sheet: 0.53 (0.25), residues: 406 loop : -0.23 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 60 HIS 0.007 0.001 HIS E 323 PHE 0.011 0.001 PHE B 473 TYR 0.009 0.001 TYR B 439 ARG 0.003 0.000 ARG B 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 1.954 Fit side-chains revert: symmetry clash REVERT: A 46 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8570 (t) REVERT: A 326 PHE cc_start: 0.7361 (m-10) cc_final: 0.6454 (p90) REVERT: B 186 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: D 223 LEU cc_start: 0.8896 (mt) cc_final: 0.8652 (mm) REVERT: E 438 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7285 (mm-30) outliers start: 20 outliers final: 16 residues processed: 123 average time/residue: 1.2674 time to fit residues: 177.0022 Evaluate side-chains 127 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 438 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.093521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.071572 restraints weight = 27362.845| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.18 r_work: 0.2791 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17634 Z= 0.181 Angle : 0.482 7.763 24030 Z= 0.245 Chirality : 0.042 0.224 2842 Planarity : 0.004 0.053 2895 Dihedral : 9.682 82.751 3138 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.12 % Allowed : 10.62 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.19), residues: 2010 helix: 3.26 (0.18), residues: 748 sheet: 0.54 (0.25), residues: 406 loop : -0.23 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 187 HIS 0.008 0.001 HIS E 323 PHE 0.012 0.001 PHE B 473 TYR 0.010 0.001 TYR B 439 ARG 0.009 0.000 ARG A 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4613.69 seconds wall clock time: 82 minutes 29.81 seconds (4949.81 seconds total)