Starting phenix.real_space_refine on Sun Mar 17 07:41:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6y_28892/03_2024/8f6y_28892_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6y_28892/03_2024/8f6y_28892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6y_28892/03_2024/8f6y_28892.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6y_28892/03_2024/8f6y_28892.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6y_28892/03_2024/8f6y_28892_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6y_28892/03_2024/8f6y_28892_updated.pdb" } resolution = 2.79 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= 0.002 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 6 5.49 5 S 85 5.16 5 C 11180 2.51 5 N 2649 2.21 5 O 3133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17053 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3140 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 366} Chain breaks: 1 Chain: "B" Number of atoms: 3463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3463 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 398} Chain breaks: 1 Chain: "C" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3315 Classifications: {'peptide': 409} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 384} Chain breaks: 1 Chain: "D" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3151 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 367} Chain breaks: 1 Chain: "E" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3346 Classifications: {'peptide': 412} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 389} Chain breaks: 1 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 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: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'CHT': 1, 'CLR': 1, 'V8D': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'NAG': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'CLR': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 97 Unusual residues: {'CHT': 1, 'CLR': 1, 'DD9': 1, 'POV': 1, 'V8D': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 87 Unusual residues: {'NAG': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 9.33, per 1000 atoms: 0.55 Number of scatterers: 17053 At special positions: 0 Unit cell: (109.824, 139.392, 156.288, 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 85 16.00 P 6 15.00 O 3133 8.00 N 2649 7.00 C 11180 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=2.04 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.01 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=2.04 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 - 3.50 Amino acid : False - 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 ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 5 " " BMA I 3 " - " MAN I 4 " " MAN I 4 " - " MAN I 5 " " 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 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-ASN " NAG B 601 " - " 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: 7.00 Conformation dependent library (CDL) restraints added in 3.0 seconds 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3908 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 23 sheets defined 39.6% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 69 through 72 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 219 through 226 Processing helix chain 'A' and resid 230 through 234 Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 242 through 263 removed outlier: 3.679A pdb=" N LEU A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 299 Processing helix chain 'A' and resid 310 through 318 removed outlier: 3.845A pdb=" N ILE A 315 " --> pdb=" O TRP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 323 No H-bonds generated for 'chain 'A' and resid 320 through 323' Processing helix chain 'A' and resid 371 through 425 Processing helix chain 'B' and resid 3 through 12 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 233 through 248 removed outlier: 3.670A pdb=" N ALA B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 276 Processing helix chain 'B' and resid 287 through 313 Processing helix chain 'B' and resid 324 through 331 Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 417 through 475 Proline residue: B 463 - end of helix Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 69 through 72 Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 218 through 239 removed outlier: 4.765A pdb=" N ILE C 226 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Proline residue: C 227 - end of helix removed outlier: 4.510A pdb=" N PHE C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 245 No H-bonds generated for 'chain 'C' and resid 243 through 245' Processing helix chain 'C' and resid 248 through 268 removed outlier: 4.166A pdb=" N ASP C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 305 Processing helix chain 'C' and resid 316 through 323 Processing helix chain 'C' and resid 326 through 330 Processing helix chain 'C' and resid 399 through 459 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 69 through 72 Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 212 through 234 removed outlier: 4.522A pdb=" N ILE D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Proline residue: D 221 - end of helix removed outlier: 4.497A pdb=" N GLY D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEU D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N PHE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR D 234 " --> pdb=" O GLY D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 239 No H-bonds generated for 'chain 'D' and resid 237 through 239' Processing helix chain 'D' and resid 242 through 263 removed outlier: 3.562A pdb=" N GLU D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU D 263 " --> pdb=" O VAL D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 299 Processing helix chain 'D' and resid 310 through 317 Processing helix chain 'D' and resid 320 through 323 No H-bonds generated for 'chain 'D' and resid 320 through 323' Processing helix chain 'D' and resid 371 through 425 Processing helix chain 'E' and resid 4 through 12 Processing helix chain 'E' and resid 69 through 72 Processing helix chain 'E' and resid 82 through 84 No H-bonds generated for 'chain 'E' and resid 82 through 84' Processing helix chain 'E' and resid 220 through 225 Processing helix chain 'E' and resid 227 through 241 removed outlier: 3.843A pdb=" N LEU E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL E 237 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LEU E 239 " --> pdb=" O SER E 235 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TYR E 241 " --> pdb=" O VAL E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 272 Processing helix chain 'E' and resid 282 through 308 Processing helix chain 'E' and resid 319 through 326 Processing helix chain 'E' and resid 328 through 332 Processing helix chain 'E' and resid 412 through 471 Processing sheet with id= A, first strand: chain 'A' and resid 156 through 160 removed outlier: 5.914A pdb=" N VAL A 29 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N SER A 159 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE A 31 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP A 30 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE A 61 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN A 53 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU A 40 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLU A 51 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 42 through 44 Processing sheet with id= C, first strand: chain 'A' and resid 77 through 81 Processing sheet with id= D, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.820A pdb=" N CYS A 142 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 205 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 180 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N MET A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 158 through 162 removed outlier: 6.353A pdb=" N VAL B 31 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ASP B 161 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE B 33 " --> pdb=" O ASP B 161 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASN B 32 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TYR B 63 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN B 55 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 44 through 46 Processing sheet with id= G, first strand: chain 'B' and resid 79 through 82 Processing sheet with id= H, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.042A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLN B 213 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 164 through 166 Processing sheet with id= J, first strand: chain 'B' and resid 190 through 194 removed outlier: 6.792A pdb=" N ILE B 220 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 156 through 160 removed outlier: 6.149A pdb=" N VAL C 29 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN C 159 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL C 31 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR C 30 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR C 61 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C 53 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR C 51 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 42 through 44 Processing sheet with id= M, first strand: chain 'C' and resid 77 through 80 Processing sheet with id= N, first strand: chain 'C' and resid 90 through 92 Processing sheet with id= O, first strand: chain 'C' and resid 186 through 190 removed outlier: 6.704A pdb=" N ILE C 212 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 156 through 160 removed outlier: 5.890A pdb=" N VAL D 29 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N SER D 159 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE D 31 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASP D 30 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE D 61 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASN D 53 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU D 40 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLU D 51 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 42 through 44 Processing sheet with id= R, first strand: chain 'D' and resid 77 through 81 Processing sheet with id= S, first strand: chain 'D' and resid 90 through 92 removed outlier: 3.719A pdb=" N CYS D 142 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE D 205 " --> pdb=" O CYS D 142 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP D 180 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLN D 208 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N MET D 178 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 156 through 160 removed outlier: 6.528A pdb=" N ILE E 29 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLN E 159 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL E 31 " --> pdb=" O GLN E 159 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASP E 30 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASN E 61 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU E 40 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU E 119 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN E 107 " --> pdb=" O LEU E 119 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 42 through 44 Processing sheet with id= V, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.225A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 184 through 188 removed outlier: 6.867A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) 789 hydrogen bonds defined for protein. 2304 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: 5.38 Time building geometry restraints manager: 7.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2648 1.31 - 1.45: 4826 1.45 - 1.58: 9869 1.58 - 1.71: 12 1.71 - 1.85: 139 Bond restraints: 17494 Sorted by residual: bond pdb=" C SER D 226 " pdb=" N PHE D 227 " ideal model delta sigma weight residual 1.335 1.386 -0.051 1.38e-02 5.25e+03 1.38e+01 bond pdb=" C PHE A 227 " pdb=" N LEU A 228 " ideal model delta sigma weight residual 1.332 1.386 -0.055 1.52e-02 4.33e+03 1.29e+01 bond pdb=" N POV B 602 " pdb=" C12 POV B 602 " ideal model delta sigma weight residual 1.508 1.446 0.062 2.00e-02 2.50e+03 9.76e+00 bond pdb=" N POV E 503 " pdb=" C12 POV E 503 " ideal model delta sigma weight residual 1.508 1.449 0.059 2.00e-02 2.50e+03 8.57e+00 bond pdb=" N POV E 502 " pdb=" C12 POV E 502 " ideal model delta sigma weight residual 1.508 1.450 0.058 2.00e-02 2.50e+03 8.29e+00 ... (remaining 17489 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.53: 590 106.53 - 113.40: 10099 113.40 - 120.27: 6231 120.27 - 127.14: 6666 127.14 - 134.02: 269 Bond angle restraints: 23855 Sorted by residual: angle pdb=" O13 POV C 502 " pdb=" P POV C 502 " pdb=" O14 POV C 502 " ideal model delta sigma weight residual 121.11 109.10 12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" O13 POV E 503 " pdb=" P POV E 503 " pdb=" O14 POV E 503 " ideal model delta sigma weight residual 121.11 109.12 11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" O13 POV D 604 " pdb=" P POV D 604 " pdb=" O14 POV D 604 " ideal model delta sigma weight residual 121.11 109.12 11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" O11 POV C 501 " pdb=" P POV C 501 " pdb=" O12 POV C 501 " ideal model delta sigma weight residual 97.67 109.55 -11.88 3.00e+00 1.11e-01 1.57e+01 angle pdb=" O11 POV C 502 " pdb=" P POV C 502 " pdb=" O12 POV C 502 " ideal model delta sigma weight residual 97.67 109.49 -11.82 3.00e+00 1.11e-01 1.55e+01 ... (remaining 23850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.29: 10508 31.29 - 62.58: 262 62.58 - 93.87: 56 93.87 - 125.16: 17 125.16 - 156.45: 2 Dihedral angle restraints: 10845 sinusoidal: 4843 harmonic: 6002 Sorted by residual: dihedral pdb=" CA CYS D 142 " pdb=" C CYS D 142 " pdb=" N THR D 143 " pdb=" CA THR D 143 " ideal model delta harmonic sigma weight residual 180.00 -150.69 -29.31 0 5.00e+00 4.00e-02 3.44e+01 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 -150.82 -29.18 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA CYS D 192 " pdb=" C CYS D 192 " pdb=" N CYS D 193 " pdb=" CA CYS D 193 " ideal model delta harmonic sigma weight residual -180.00 -151.55 -28.45 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 10842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2673 0.103 - 0.207: 127 0.207 - 0.310: 7 0.310 - 0.414: 1 0.414 - 0.517: 1 Chirality restraints: 2809 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.96e+01 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 -2.32 -0.08 2.00e-02 2.50e+03 1.41e+01 chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 208 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.68e+00 ... (remaining 2806 not shown) Planarity restraints: 2892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 141 " 0.028 2.00e-02 2.50e+03 2.87e-02 1.03e+01 pdb=" CG ASN C 141 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN C 141 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 141 " -0.045 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 V8D D 601 " -0.027 2.00e-02 2.50e+03 2.30e-02 9.27e+00 pdb=" C08 V8D D 601 " -0.011 2.00e-02 2.50e+03 pdb=" C09 V8D D 601 " 0.033 2.00e-02 2.50e+03 pdb=" C12 V8D D 601 " -0.031 2.00e-02 2.50e+03 pdb=" C13 V8D D 601 " 0.026 2.00e-02 2.50e+03 pdb=" N03 V8D D 601 " 0.011 2.00e-02 2.50e+03 pdb=" N04 V8D D 601 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " -0.024 2.00e-02 2.50e+03 2.00e-02 5.00e+00 pdb=" C7 NAG H 2 " 0.009 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " -0.019 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " 0.030 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.004 2.00e-02 2.50e+03 ... (remaining 2889 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 146 2.64 - 3.21: 15495 3.21 - 3.77: 25315 3.77 - 4.34: 36759 4.34 - 4.90: 61166 Nonbonded interactions: 138881 Sorted by model distance: nonbonded pdb=" NH2 ARG E 147 " pdb=" OE2 GLU E 208 " model vdw 2.076 2.520 nonbonded pdb=" OG SER A 82 " pdb=" O THR A 106 " model vdw 2.076 2.440 nonbonded pdb=" ND2 ASN B 305 " pdb=" OG SER B 457 " model vdw 2.108 2.520 nonbonded pdb=" OD2 ASP D 44 " pdb=" ND2 ASN D 47 " model vdw 2.138 2.520 nonbonded pdb=" OD2 ASP B 140 " pdb=" NE2 GLN B 142 " model vdw 2.151 2.520 ... (remaining 138876 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'D' and (resid 1 through 330 or resid 370 through 426 or resid 601 throug \ h 603)) } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'J' } 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=1.00 max=1.00 mean=1.00 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: 1.170 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: 0.030 Extract box with map and model: 5.920 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 47.260 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.100 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:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 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 : 0.007 0.062 17494 Z= 0.453 Angle : 0.756 12.012 23855 Z= 0.340 Chirality : 0.049 0.517 2809 Planarity : 0.004 0.035 2885 Dihedral : 15.563 156.455 6916 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: 0.98 (0.19), residues: 2002 helix: 2.69 (0.18), residues: 764 sheet: -0.67 (0.25), residues: 401 loop : -0.58 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 118 HIS 0.010 0.001 HIS B 103 PHE 0.014 0.001 PHE A 225 TYR 0.015 0.001 TYR C 410 ARG 0.006 0.001 ARG E 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.969 Fit side-chains REVERT: A 97 ASP cc_start: 0.8039 (t70) cc_final: 0.7670 (t0) REVERT: E 332 TYR cc_start: 0.8347 (m-80) cc_final: 0.8027 (m-10) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 1.5340 time to fit residues: 159.6715 Evaluate side-chains 68 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 0.9980 chunk 150 optimal weight: 0.0770 chunk 83 optimal weight: 2.9990 chunk 51 optimal weight: 0.0970 chunk 101 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 180 optimal weight: 0.7980 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 HIS B 276 GLN B 305 ASN C 39 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17494 Z= 0.158 Angle : 0.510 6.702 23855 Z= 0.257 Chirality : 0.043 0.317 2809 Planarity : 0.003 0.039 2885 Dihedral : 12.219 126.635 2993 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.80 % Allowed : 4.28 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: 1.57 (0.19), residues: 2002 helix: 3.21 (0.18), residues: 765 sheet: -0.27 (0.24), residues: 413 loop : -0.34 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 311 HIS 0.003 0.001 HIS C 112 PHE 0.020 0.001 PHE D 316 TYR 0.011 0.001 TYR B 439 ARG 0.008 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 1.840 Fit side-chains REVERT: A 97 ASP cc_start: 0.7985 (t70) cc_final: 0.7611 (t0) outliers start: 15 outliers final: 4 residues processed: 80 average time/residue: 1.4333 time to fit residues: 128.5393 Evaluate side-chains 72 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 CYS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain D residue 222 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 181 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 161 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 61 optimal weight: 0.0060 chunk 145 optimal weight: 3.9990 overall best weight: 2.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 17494 Z= 0.298 Angle : 0.504 6.791 23855 Z= 0.253 Chirality : 0.043 0.308 2809 Planarity : 0.003 0.034 2885 Dihedral : 10.816 108.241 2993 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.59 % Allowed : 6.58 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: 1.68 (0.19), residues: 2002 helix: 3.29 (0.18), residues: 764 sheet: -0.08 (0.25), residues: 410 loop : -0.35 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 187 HIS 0.007 0.001 HIS B 103 PHE 0.014 0.001 PHE D 280 TYR 0.011 0.001 TYR B 439 ARG 0.005 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 2.147 Fit side-chains REVERT: A 97 ASP cc_start: 0.8067 (t70) cc_final: 0.7668 (t0) REVERT: A 278 MET cc_start: 0.9098 (mmt) cc_final: 0.8889 (mmt) REVERT: D 310 GLN cc_start: 0.8798 (tp40) cc_final: 0.8410 (tp-100) REVERT: E 448 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8391 (t0) outliers start: 11 outliers final: 5 residues processed: 76 average time/residue: 1.3927 time to fit residues: 119.4116 Evaluate side-chains 75 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 466 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 178 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 121 optimal weight: 0.0980 chunk 181 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 431 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17494 Z= 0.156 Angle : 0.452 6.694 23855 Z= 0.229 Chirality : 0.042 0.287 2809 Planarity : 0.003 0.035 2885 Dihedral : 9.534 98.788 2993 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.70 % Allowed : 7.11 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: 2002 helix: 3.46 (0.18), residues: 761 sheet: 0.17 (0.25), residues: 404 loop : -0.33 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 311 HIS 0.003 0.000 HIS D 204 PHE 0.012 0.001 PHE D 280 TYR 0.013 0.001 TYR D 190 ARG 0.004 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 1.899 Fit side-chains REVERT: A 97 ASP cc_start: 0.8034 (t70) cc_final: 0.7644 (t0) REVERT: D 310 GLN cc_start: 0.8783 (tp40) cc_final: 0.8390 (tp-100) REVERT: D 407 ASP cc_start: 0.8512 (t0) cc_final: 0.8294 (t0) REVERT: E 448 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8359 (t0) outliers start: 13 outliers final: 6 residues processed: 86 average time/residue: 1.3885 time to fit residues: 134.0366 Evaluate side-chains 78 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 466 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 98 optimal weight: 0.0980 chunk 172 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.8817 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 0.037 17494 Z= 0.206 Angle : 0.457 6.699 23855 Z= 0.230 Chirality : 0.042 0.281 2809 Planarity : 0.003 0.044 2885 Dihedral : 9.063 98.559 2993 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.80 % Allowed : 7.91 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: 1.91 (0.19), residues: 2002 helix: 3.45 (0.18), residues: 762 sheet: 0.20 (0.25), residues: 410 loop : -0.27 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 311 HIS 0.004 0.001 HIS B 103 PHE 0.013 0.001 PHE D 280 TYR 0.010 0.001 TYR B 439 ARG 0.007 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 2.015 Fit side-chains REVERT: A 97 ASP cc_start: 0.8066 (t70) cc_final: 0.7674 (t0) REVERT: C 436 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8458 (t0) outliers start: 15 outliers final: 6 residues processed: 82 average time/residue: 1.3766 time to fit residues: 126.7957 Evaluate side-chains 75 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 436 ASP Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 466 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 4.9990 chunk 173 optimal weight: 0.0870 chunk 38 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 16 optimal weight: 0.0870 chunk 63 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17494 Z= 0.139 Angle : 0.441 7.664 23855 Z= 0.222 Chirality : 0.041 0.265 2809 Planarity : 0.003 0.042 2885 Dihedral : 8.513 94.944 2993 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.64 % Allowed : 8.34 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: 2.02 (0.20), residues: 2002 helix: 3.51 (0.18), residues: 762 sheet: 0.36 (0.25), residues: 411 loop : -0.23 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 311 HIS 0.003 0.000 HIS D 204 PHE 0.012 0.001 PHE D 280 TYR 0.010 0.001 TYR B 439 ARG 0.012 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 2.005 Fit side-chains REVERT: A 97 ASP cc_start: 0.8022 (t70) cc_final: 0.7644 (t0) REVERT: C 436 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8503 (t0) REVERT: E 448 ASP cc_start: 0.8279 (t0) cc_final: 0.7958 (t0) outliers start: 12 outliers final: 7 residues processed: 79 average time/residue: 1.4387 time to fit residues: 127.3983 Evaluate side-chains 76 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 436 ASP Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 466 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 185 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 GLN ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17494 Z= 0.270 Angle : 0.479 7.089 23855 Z= 0.240 Chirality : 0.042 0.276 2809 Planarity : 0.003 0.052 2885 Dihedral : 8.324 95.970 2993 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.75 % Allowed : 8.72 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: 1.96 (0.20), residues: 2002 helix: 3.47 (0.18), residues: 762 sheet: 0.29 (0.25), residues: 405 loop : -0.26 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 311 HIS 0.004 0.001 HIS B 103 PHE 0.013 0.001 PHE D 280 TYR 0.011 0.001 TYR B 439 ARG 0.014 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 2.060 Fit side-chains REVERT: A 97 ASP cc_start: 0.8083 (t70) cc_final: 0.7718 (t0) REVERT: A 278 MET cc_start: 0.8820 (mmt) cc_final: 0.8575 (mtt) REVERT: C 436 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8479 (t0) REVERT: E 448 ASP cc_start: 0.8451 (t0) cc_final: 0.8059 (t0) outliers start: 14 outliers final: 7 residues processed: 80 average time/residue: 1.4369 time to fit residues: 129.1317 Evaluate side-chains 77 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 436 ASP Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 466 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 118 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 174 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17494 Z= 0.267 Angle : 0.488 11.721 23855 Z= 0.244 Chirality : 0.042 0.287 2809 Planarity : 0.003 0.055 2885 Dihedral : 8.139 96.152 2993 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.70 % Allowed : 8.93 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: 1.91 (0.20), residues: 2002 helix: 3.44 (0.18), residues: 760 sheet: 0.24 (0.25), residues: 406 loop : -0.27 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 60 HIS 0.004 0.001 HIS B 60 PHE 0.013 0.001 PHE D 280 TYR 0.011 0.001 TYR B 439 ARG 0.013 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 2.194 Fit side-chains REVERT: A 97 ASP cc_start: 0.8092 (t70) cc_final: 0.7742 (t0) REVERT: A 278 MET cc_start: 0.8855 (mmt) cc_final: 0.8630 (mtt) REVERT: C 436 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8460 (t0) REVERT: E 448 ASP cc_start: 0.8472 (t0) cc_final: 0.8065 (t0) outliers start: 13 outliers final: 7 residues processed: 80 average time/residue: 1.3923 time to fit residues: 125.4774 Evaluate side-chains 76 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 436 ASP Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 466 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 178 optimal weight: 0.0980 chunk 107 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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: 0.8810 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17494 Z= 0.171 Angle : 0.454 6.681 23855 Z= 0.229 Chirality : 0.042 0.277 2809 Planarity : 0.003 0.058 2885 Dihedral : 7.859 92.760 2993 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.48 % Allowed : 9.25 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: 2.01 (0.20), residues: 2002 helix: 3.49 (0.18), residues: 761 sheet: 0.33 (0.25), residues: 410 loop : -0.20 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 311 HIS 0.003 0.000 HIS D 204 PHE 0.012 0.001 PHE B 294 TYR 0.010 0.001 TYR B 439 ARG 0.013 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 1.700 Fit side-chains REVERT: A 97 ASP cc_start: 0.8076 (t70) cc_final: 0.7724 (t0) REVERT: A 278 MET cc_start: 0.8794 (mmt) cc_final: 0.8587 (mtt) REVERT: C 436 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8478 (t0) REVERT: E 448 ASP cc_start: 0.8456 (t0) cc_final: 0.8060 (t0) outliers start: 9 outliers final: 7 residues processed: 77 average time/residue: 1.4363 time to fit residues: 123.9153 Evaluate side-chains 76 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 436 ASP Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 115 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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: 0.8827 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17494 Z= 0.244 Angle : 0.475 7.990 23855 Z= 0.238 Chirality : 0.042 0.279 2809 Planarity : 0.003 0.064 2885 Dihedral : 7.801 92.166 2993 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.53 % Allowed : 9.36 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: 1.96 (0.20), residues: 2002 helix: 3.49 (0.18), residues: 760 sheet: 0.25 (0.25), residues: 408 loop : -0.23 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 311 HIS 0.004 0.001 HIS B 103 PHE 0.011 0.001 PHE D 280 TYR 0.011 0.001 TYR B 439 ARG 0.015 0.000 ARG C 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 2.043 Fit side-chains REVERT: A 97 ASP cc_start: 0.8113 (t70) cc_final: 0.7762 (t0) REVERT: A 278 MET cc_start: 0.8824 (mmt) cc_final: 0.8608 (mtt) REVERT: C 436 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8463 (t0) REVERT: E 448 ASP cc_start: 0.8473 (t0) cc_final: 0.8070 (t0) outliers start: 10 outliers final: 8 residues processed: 77 average time/residue: 1.5300 time to fit residues: 131.6008 Evaluate side-chains 78 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 436 ASP Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 48 optimal weight: 0.4980 chunk 145 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.3111 r_free = 0.3111 target = 0.061560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.045840 restraints weight = 46833.313| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 3.40 r_work: 0.2538 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17494 Z= 0.175 Angle : 0.459 13.433 23855 Z= 0.229 Chirality : 0.041 0.271 2809 Planarity : 0.003 0.061 2885 Dihedral : 7.531 89.383 2993 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.48 % Allowed : 9.41 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: 2.03 (0.20), residues: 2002 helix: 3.52 (0.18), residues: 761 sheet: 0.32 (0.25), residues: 406 loop : -0.20 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 311 HIS 0.003 0.000 HIS D 204 PHE 0.010 0.001 PHE D 280 TYR 0.010 0.001 TYR B 439 ARG 0.015 0.000 ARG C 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3762.98 seconds wall clock time: 68 minutes 28.49 seconds (4108.49 seconds total)