Starting phenix.real_space_refine (version: 1.21rc1) on Sun Oct 8 16:12:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6y_28892/10_2023/8f6y_28892_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6y_28892/10_2023/8f6y_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_28892/10_2023/8f6y_28892.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6y_28892/10_2023/8f6y_28892.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6y_28892/10_2023/8f6y_28892_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6y_28892/10_2023/8f6y_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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 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 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 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 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 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: 15 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: 31 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: 9.11, per 1000 atoms: 0.53 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: 7.02 Conformation dependent library (CDL) restraints added in 2.3 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: 2.70 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: 5.58 Time building geometry restraints manager: 7.51 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: 9915 31.29 - 62.58: 232 62.58 - 93.87: 29 93.87 - 125.16: 1 125.16 - 156.45: 2 Dihedral angle restraints: 10179 sinusoidal: 4177 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 10176 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: 1.230 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: 5.890 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 44.940 Find NCS groups from input model: 0.920 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:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.270 ------------------------------------------------------------------------------- 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 : 14.028 156.455 6250 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 *********************** 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 : 2.138 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 1.5927 time to fit residues: 166.3898 Evaluate side-chains 67 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.857 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3638 ------------------------------------------------------------------------------- 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: 0.8801 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17494 Z= 0.159 Angle : 0.496 6.704 23855 Z= 0.253 Chirality : 0.043 0.323 2809 Planarity : 0.003 0.036 2885 Dihedral : 10.083 130.107 2327 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.75 % Allowed : 4.39 % Favored : 94.87 % 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: -0.23 (0.24), residues: 403 loop : -0.36 (0.22), residues: 834 *********************** 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 87 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 2.058 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 79 average time/residue: 1.5010 time to fit residues: 132.9656 Evaluate side-chains 74 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 1.959 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.6607 time to fit residues: 4.9965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 123 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 181 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 61 optimal weight: 0.0770 chunk 145 optimal weight: 3.9990 overall best weight: 2.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 ASN E 431 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 17494 Z= 0.371 Angle : 0.528 6.881 23855 Z= 0.268 Chirality : 0.043 0.327 2809 Planarity : 0.003 0.034 2885 Dihedral : 9.547 113.719 2327 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.75 % Allowed : 6.52 % Favored : 92.73 % 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: 1.60 (0.19), residues: 2002 helix: 3.22 (0.18), residues: 765 sheet: -0.13 (0.25), residues: 407 loop : -0.40 (0.22), residues: 830 *********************** 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 83 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 1.956 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 76 average time/residue: 1.3907 time to fit residues: 119.0512 Evaluate side-chains 71 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 1.782 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.2979 time to fit residues: 3.0295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 93 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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: 0.8834 moved from start: 0.1354 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= 0.238 Angle : 0.474 6.787 23855 Z= 0.242 Chirality : 0.042 0.307 2809 Planarity : 0.003 0.035 2885 Dihedral : 8.877 103.226 2327 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.75 % Allowed : 7.38 % Favored : 91.87 % 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: 1.72 (0.19), residues: 2002 helix: 3.31 (0.18), residues: 763 sheet: 0.03 (0.25), residues: 407 loop : -0.35 (0.22), residues: 832 *********************** 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 85 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 1.872 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 81 average time/residue: 1.3857 time to fit residues: 126.6145 Evaluate side-chains 72 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 2.173 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.7987 time to fit residues: 4.7386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 0.4980 chunk 109 optimal weight: 0.9980 chunk 2 optimal weight: 0.0470 chunk 143 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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: 0.8800 moved from start: 0.1641 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= 0.141 Angle : 0.440 7.376 23855 Z= 0.224 Chirality : 0.041 0.278 2809 Planarity : 0.003 0.039 2885 Dihedral : 8.123 97.011 2327 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.59 % Allowed : 8.29 % Favored : 91.12 % 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: 1.95 (0.20), residues: 2002 helix: 3.48 (0.18), residues: 762 sheet: 0.32 (0.25), residues: 406 loop : -0.30 (0.22), residues: 834 *********************** 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 85 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 1.964 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 83 average time/residue: 1.4836 time to fit residues: 138.3293 Evaluate side-chains 72 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 2.193 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.3511 time to fit residues: 3.2522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 38 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.8818 moved from start: 0.1682 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= 0.206 Angle : 0.450 6.695 23855 Z= 0.228 Chirality : 0.041 0.278 2809 Planarity : 0.003 0.048 2885 Dihedral : 7.874 96.658 2327 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.86 % Allowed : 8.66 % Favored : 90.48 % 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: 762 sheet: 0.27 (0.25), residues: 410 loop : -0.27 (0.22), residues: 830 *********************** 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 84 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 1.803 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 81 average time/residue: 1.3799 time to fit residues: 126.2517 Evaluate side-chains 75 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 2.060 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.7481 time to fit residues: 4.3696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 185 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 191 optimal weight: 0.0070 chunk 120 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 408 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1806 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= 0.166 Angle : 0.448 10.295 23855 Z= 0.227 Chirality : 0.041 0.269 2809 Planarity : 0.003 0.049 2885 Dihedral : 7.579 94.395 2327 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.86 % Allowed : 8.93 % Favored : 90.21 % 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: 2.00 (0.20), residues: 2002 helix: 3.51 (0.18), residues: 762 sheet: 0.33 (0.25), residues: 410 loop : -0.26 (0.22), residues: 830 *********************** 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 85 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 2.068 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 82 average time/residue: 1.4373 time to fit residues: 132.6156 Evaluate side-chains 75 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 2.012 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.3238 time to fit residues: 3.1139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 118 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN B 276 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 17494 Z= 0.458 Angle : 0.569 6.887 23855 Z= 0.286 Chirality : 0.044 0.320 2809 Planarity : 0.003 0.060 2885 Dihedral : 7.834 100.090 2327 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.75 % Allowed : 9.36 % Favored : 89.89 % 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: 1.73 (0.19), residues: 2002 helix: 3.28 (0.18), residues: 763 sheet: 0.21 (0.26), residues: 398 loop : -0.40 (0.22), residues: 841 *********************** 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 79 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 2.029 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 75 average time/residue: 1.4465 time to fit residues: 122.3991 Evaluate side-chains 75 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 1.963 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.9100 time to fit residues: 5.8122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 161 optimal weight: 0.7980 chunk 169 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 189 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8822 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17494 Z= 0.164 Angle : 0.469 9.800 23855 Z= 0.237 Chirality : 0.041 0.295 2809 Planarity : 0.003 0.057 2885 Dihedral : 7.558 95.737 2327 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.59 % Allowed : 9.52 % Favored : 89.89 % 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: 1.94 (0.20), residues: 2002 helix: 3.49 (0.18), residues: 760 sheet: 0.22 (0.25), residues: 413 loop : -0.27 (0.22), residues: 829 *********************** 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 80 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 2.026 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 78 average time/residue: 1.5077 time to fit residues: 132.2520 Evaluate side-chains 74 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 2.085 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.3481 time to fit residues: 3.2329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 115 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 198 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 96 optimal weight: 0.2980 chunk 125 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 310 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1969 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= 0.163 Angle : 0.450 7.875 23855 Z= 0.228 Chirality : 0.041 0.275 2809 Planarity : 0.003 0.058 2885 Dihedral : 7.292 89.793 2327 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.43 % Allowed : 9.68 % Favored : 89.89 % 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: 2.00 (0.20), residues: 2002 helix: 3.52 (0.18), residues: 763 sheet: 0.27 (0.25), residues: 413 loop : -0.23 (0.22), residues: 826 ********************** 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 78 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 1.981 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 76 average time/residue: 1.5135 time to fit residues: 129.0203 Evaluate side-chains 74 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 2.095 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 1 average time/residue: 1.3382 time to fit residues: 4.2487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 48 optimal weight: 0.3980 chunk 145 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- 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 = 0.3100 r_free = 0.3100 target = 0.060875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.045283 restraints weight = 47219.380| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 3.37 r_work: 0.2534 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17494 Z= 0.196 Angle : 0.456 7.646 23855 Z= 0.231 Chirality : 0.041 0.275 2809 Planarity : 0.003 0.062 2885 Dihedral : 7.263 88.547 2327 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.43 % Allowed : 9.79 % Favored : 89.79 % 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: 3.55 (0.18), residues: 761 sheet: 0.26 (0.25), residues: 408 loop : -0.23 (0.22), residues: 833 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3739.07 seconds wall clock time: 68 minutes 43.57 seconds (4123.57 seconds total)