Starting phenix.real_space_refine on Mon Nov 18 22:53:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6z_28893/11_2024/8f6z_28893.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6z_28893/11_2024/8f6z_28893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6z_28893/11_2024/8f6z_28893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6z_28893/11_2024/8f6z_28893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6z_28893/11_2024/8f6z_28893.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6z_28893/11_2024/8f6z_28893.cif" } resolution = 2.7 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 85 5.16 5 C 11129 2.51 5 N 2640 2.21 5 O 3138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 16997 Number of models: 1 Model: "" Number of chains: 19 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: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3456 Classifications: {'peptide': 425} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 397} Chain breaks: 1 Chain: "C" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3294 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 382} Chain breaks: 1 Chain: "D" Number of atoms: 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: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3317 Classifications: {'peptide': 409} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 386} 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: "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: "K" 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'CLR': 1, 'SCK': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {'DD9': 1, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {'CLR': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'CLR': 1, 'POV': 1, 'SCK': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'NAG': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 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} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1 CLR A 502 " occ=0.80 ... (26 atoms not shown) pdb=" O1 CLR A 502 " occ=0.80 residue: pdb=" N POV B 602 " occ=0.75 ... (35 atoms not shown) pdb="C311 POV B 602 " occ=0.75 residue: pdb=" C1 CLR C 501 " occ=0.89 ... (26 atoms not shown) pdb=" O1 CLR C 501 " occ=0.89 residue: pdb=" C1 CLR D 503 " occ=0.75 ... (26 atoms not shown) pdb=" O1 CLR D 503 " occ=0.75 Time building chain proxies: 10.57, per 1000 atoms: 0.62 Number of scatterers: 16997 At special positions: 0 Unit cell: (99.4542, 111.218, 164.688, 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 5 15.00 O 3138 8.00 N 2640 7.00 C 11129 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=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.02 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 5 " " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " " BMA K 3 " - " MAN K 4 " " MAN K 4 " - " MAN K 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG B 601 " - " ASN B 70 " " NAG E 501 " - " ASN E 68 " " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 143 " " NAG H 1 " - " ASN B 208 " " NAG I 1 " - " ASN C 141 " " NAG J 1 " - " ASN D 141 " " NAG K 1 " - " ASN E 141 " Time building additional restraints: 5.18 Conformation dependent library (CDL) restraints added in 2.0 seconds 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3894 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 20 sheets defined 43.7% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 63 through 66 removed outlier: 3.563A pdb=" N ARG A 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 68 through 73 removed outlier: 4.232A pdb=" N GLY A 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 212 through 218 Processing helix chain 'A' and resid 218 through 235 removed outlier: 4.053A pdb=" N THR A 229 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 241 through 262 Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 317 removed outlier: 3.726A pdb=" N ILE A 315 " --> pdb=" O TRP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 371 through 426 removed outlier: 3.507A pdb=" N ALA A 375 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 232 through 246 removed outlier: 3.713A pdb=" N ALA B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 250 through 254 removed outlier: 3.619A pdb=" N GLY B 254 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 276 Processing helix chain 'B' and resid 286 through 314 Processing helix chain 'B' and resid 323 through 332 removed outlier: 3.656A pdb=" N GLU B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 removed outlier: 4.196A pdb=" N ARG B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 478 removed outlier: 3.653A pdb=" N SER B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) Proline residue: B 463 - end of helix removed outlier: 3.811A pdb=" N ASN B 477 " --> pdb=" O PHE B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 68 through 73 removed outlier: 4.091A pdb=" N GLU C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.532A pdb=" N VAL C 85 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 180 removed outlier: 3.900A pdb=" N PHE C 180 " --> pdb=" O LYS C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 180' Processing helix chain 'C' and resid 217 through 238 removed outlier: 4.639A pdb=" N ILE C 226 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 247 through 267 Processing helix chain 'C' and resid 278 through 306 Processing helix chain 'C' and resid 315 through 324 removed outlier: 3.585A pdb=" N GLU C 324 " --> pdb=" O GLN C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 331 removed outlier: 4.163A pdb=" N PHE C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 460 Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 63 through 66 Processing helix chain 'D' and resid 68 through 73 removed outlier: 4.037A pdb=" N GLY D 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 218 through 230 removed outlier: 4.006A pdb=" N GLY D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 236 through 240 Processing helix chain 'D' and resid 241 through 262 removed outlier: 3.834A pdb=" N GLU D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 300 Processing helix chain 'D' and resid 309 through 317 Processing helix chain 'D' and resid 319 through 323 Processing helix chain 'D' and resid 371 through 426 removed outlier: 3.613A pdb=" N PHE D 426 " --> pdb=" O THR D 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 removed outlier: 4.180A pdb=" N ARG E 6 " --> pdb=" O ASN E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 removed outlier: 3.993A pdb=" N GLU E 73 " --> pdb=" O SER E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 219 through 226 Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 236 through 243 Processing helix chain 'E' and resid 250 through 271 removed outlier: 3.628A pdb=" N GLN E 271 " --> pdb=" O PHE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 309 Processing helix chain 'E' and resid 318 through 328 removed outlier: 3.615A pdb=" N PHE E 328 " --> pdb=" O LEU E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 472 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.130A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.130A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE A 49 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL A 43 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU A 51 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG A 55 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU A 37 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG A 57 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LEU A 35 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLN A 59 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL A 33 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N ILE A 61 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE A 31 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.716A pdb=" N CYS A 142 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N MET A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 82 removed outlier: 4.602A pdb=" N GLY B 116 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR B 51 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER B 44 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN B 55 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR B 63 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASN B 32 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 123 through 129 removed outlier: 6.808A pdb=" N THR B 51 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER B 44 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN B 55 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR B 63 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASN B 32 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N ILE B 178 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU B 37 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 94 removed outlier: 4.686A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLN B 213 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 220 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 94 removed outlier: 4.686A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLN B 213 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 80 removed outlier: 3.868A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN C 53 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU C 40 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N PHE C 55 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR C 38 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASN C 57 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N THR C 36 " --> pdb=" O ASN C 57 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ALA C 59 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLY C 34 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N THR C 61 " --> pdb=" O ARG C 32 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N ARG C 32 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL C 29 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLN C 159 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL C 31 " --> pdb=" O GLN C 159 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 121 through 127 removed outlier: 6.807A pdb=" N ASN C 53 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU C 40 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N PHE C 55 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR C 38 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASN C 57 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N THR C 36 " --> pdb=" O ASN C 57 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ALA C 59 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLY C 34 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N THR C 61 " --> pdb=" O ARG C 32 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N ARG C 32 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N VAL C 174 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU C 35 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.150A pdb=" N SER C 148 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLU C 205 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE C 212 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.150A pdb=" N SER C 148 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLU C 205 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N TYR C 204 " --> pdb=" O ARG C 198 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG C 198 " --> pdb=" O TYR C 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 80 removed outlier: 4.216A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 80 removed outlier: 4.216A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE D 49 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL D 43 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLU D 51 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG D 55 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU D 37 " --> pdb=" O ARG D 55 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG D 57 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU D 35 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N GLN D 59 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL D 33 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ILE D 61 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE D 31 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 90 through 92 removed outlier: 3.772A pdb=" N CYS D 142 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N TYR D 198 " --> pdb=" O TRP D 187 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP D 187 " --> pdb=" O TYR D 198 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP D 200 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LYS D 185 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N THR D 202 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY D 183 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N HIS D 204 " --> pdb=" O TYR D 181 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR D 181 " --> pdb=" O HIS D 204 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE D 206 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.822A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.822A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA E 49 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N SER E 42 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU E 40 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN E 61 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASP E 30 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE E 29 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLN E 159 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL E 31 " --> pdb=" O GLN E 159 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.232A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.232A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 162 through 163 921 hydrogen bonds defined for protein. 2646 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: 5.68 Time building geometry restraints manager: 5.77 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: 2644 1.31 - 1.44: 4786 1.44 - 1.58: 9853 1.58 - 1.71: 13 1.71 - 1.84: 139 Bond restraints: 17435 Sorted by residual: bond pdb=" C31 POV B 602 " pdb=" O31 POV B 602 " ideal model delta sigma weight residual 1.327 1.402 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C31 POV C 503 " pdb=" O31 POV C 503 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C31 POV C 502 " pdb=" O31 POV C 502 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C21 POV C 503 " pdb=" O21 POV C 503 " ideal model delta sigma weight residual 1.330 1.401 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C21 POV B 602 " pdb=" O21 POV B 602 " ideal model delta sigma weight residual 1.330 1.400 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 17430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 23384 2.62 - 5.25: 328 5.25 - 7.87: 47 7.87 - 10.50: 12 10.50 - 13.12: 10 Bond angle restraints: 23781 Sorted by residual: angle pdb=" O11 POV E 502 " pdb=" P POV E 502 " pdb=" O12 POV E 502 " ideal model delta sigma weight residual 97.67 110.79 -13.12 3.00e+00 1.11e-01 1.91e+01 angle pdb=" O11 POV C 502 " pdb=" P POV C 502 " pdb=" O12 POV C 502 " ideal model delta sigma weight residual 97.67 109.91 -12.24 3.00e+00 1.11e-01 1.66e+01 angle pdb=" O13 POV C 502 " pdb=" P POV C 502 " pdb=" O14 POV C 502 " ideal model delta sigma weight residual 121.11 109.06 12.05 3.00e+00 1.11e-01 1.61e+01 angle pdb=" O11 POV C 503 " pdb=" P POV C 503 " pdb=" O12 POV C 503 " ideal model delta sigma weight residual 97.67 109.61 -11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O11 POV B 602 " pdb=" P POV B 602 " pdb=" O12 POV B 602 " ideal model delta sigma weight residual 97.67 109.52 -11.85 3.00e+00 1.11e-01 1.56e+01 ... (remaining 23776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.83: 10485 29.83 - 59.67: 281 59.67 - 89.50: 67 89.50 - 119.34: 20 119.34 - 149.17: 2 Dihedral angle restraints: 10855 sinusoidal: 4875 harmonic: 5980 Sorted by residual: 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 -150.93 -29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA GLU B 418 " pdb=" C GLU B 418 " pdb=" N ILE B 419 " pdb=" CA ILE B 419 " ideal model delta harmonic sigma weight residual -180.00 -151.88 -28.12 0 5.00e+00 4.00e-02 3.16e+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 -153.50 -26.50 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 10852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2353 0.059 - 0.118: 409 0.118 - 0.176: 44 0.176 - 0.235: 2 0.235 - 0.294: 7 Chirality restraints: 2815 Sorted by residual: chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2812 not shown) Planarity restraints: 2881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 483 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO E 484 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO E 484 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 484 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 223 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" C ILE E 223 " -0.038 2.00e-02 2.50e+03 pdb=" O ILE E 223 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE E 224 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 393 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.78e+00 pdb=" C SER A 393 " -0.034 2.00e-02 2.50e+03 pdb=" O SER A 393 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN A 394 " 0.011 2.00e-02 2.50e+03 ... (remaining 2878 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 91 2.51 - 3.10: 12885 3.10 - 3.70: 26834 3.70 - 4.30: 40888 4.30 - 4.90: 67704 Nonbonded interactions: 148402 Sorted by model distance: nonbonded pdb=" OG SER B 244 " pdb=" OG1 THR B 462 " model vdw 1.907 3.040 nonbonded pdb=" OD1 ASN B 98 " pdb=" OG SER B 129 " model vdw 2.032 3.040 nonbonded pdb=" OD2 ASP A 152 " pdb=" OG1 THR A 154 " model vdw 2.070 3.040 nonbonded pdb=" OG SER A 82 " pdb=" O THR A 106 " model vdw 2.085 3.040 nonbonded pdb=" OD2 ASP D 138 " pdb=" NE2 GLN D 140 " model vdw 2.107 3.120 ... (remaining 148397 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 426 or resid 501)) selection = (chain 'D' and (resid 1 through 330 or resid 370 through 426 or resid 501)) } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 max=1.00 mean=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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 39.920 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 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 0.075 17435 Z= 0.438 Angle : 0.802 13.119 23781 Z= 0.368 Chirality : 0.047 0.294 2815 Planarity : 0.004 0.056 2873 Dihedral : 15.710 149.173 6940 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.19), residues: 1995 helix: 1.84 (0.19), residues: 756 sheet: -0.92 (0.24), residues: 389 loop : -0.68 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 118 HIS 0.004 0.001 HIS B 103 PHE 0.015 0.002 PHE C 12 TYR 0.015 0.002 TYR C 223 ARG 0.009 0.001 ARG E 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 1.5901 time to fit residues: 161.1798 Evaluate side-chains 74 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 179 optimal weight: 0.0170 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS B 20 HIS B 276 GLN D 204 HIS D 385 HIS E 172 HIS ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN E 437 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17435 Z= 0.195 Angle : 0.554 6.616 23781 Z= 0.279 Chirality : 0.044 0.177 2815 Planarity : 0.004 0.041 2873 Dihedral : 11.865 128.591 3031 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.86 % Allowed : 4.51 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.19), residues: 1995 helix: 2.29 (0.18), residues: 773 sheet: -0.78 (0.24), residues: 388 loop : -0.47 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 187 HIS 0.003 0.001 HIS B 60 PHE 0.012 0.001 PHE E 467 TYR 0.018 0.001 TYR E 117 ARG 0.010 0.001 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.6558 (t0) cc_final: 0.6223 (t0) REVERT: D 324 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7514 (mtp) REVERT: D 404 MET cc_start: 0.8960 (tmm) cc_final: 0.8745 (tmt) REVERT: E 116 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8195 (mmm) outliers start: 16 outliers final: 6 residues processed: 92 average time/residue: 1.5319 time to fit residues: 157.8080 Evaluate side-chains 81 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain E residue 116 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 122 optimal weight: 0.0070 chunk 49 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 160 optimal weight: 0.0570 chunk 178 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN B 276 GLN D 3 HIS D 310 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17435 Z= 0.210 Angle : 0.504 7.323 23781 Z= 0.254 Chirality : 0.043 0.163 2815 Planarity : 0.003 0.037 2873 Dihedral : 10.172 127.337 3031 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.02 % Allowed : 6.01 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 1995 helix: 2.55 (0.18), residues: 776 sheet: -0.76 (0.24), residues: 380 loop : -0.43 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 187 HIS 0.003 0.001 HIS B 60 PHE 0.012 0.001 PHE E 467 TYR 0.013 0.001 TYR B 439 ARG 0.007 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 1.876 Fit side-chains REVERT: A 373 LYS cc_start: 0.6868 (mmtt) cc_final: 0.6602 (mmtt) REVERT: D 404 MET cc_start: 0.8988 (tmm) cc_final: 0.8590 (tmt) REVERT: E 116 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8200 (mmm) outliers start: 19 outliers final: 4 residues processed: 86 average time/residue: 1.5667 time to fit residues: 149.9921 Evaluate side-chains 79 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain E residue 116 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN B 276 GLN D 48 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17435 Z= 0.227 Angle : 0.498 6.540 23781 Z= 0.251 Chirality : 0.043 0.197 2815 Planarity : 0.003 0.035 2873 Dihedral : 9.293 123.630 3031 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.61 % Allowed : 6.55 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.19), residues: 1995 helix: 2.70 (0.18), residues: 777 sheet: -0.67 (0.24), residues: 396 loop : -0.33 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 311 HIS 0.004 0.001 HIS B 60 PHE 0.011 0.001 PHE E 467 TYR 0.012 0.001 TYR B 439 ARG 0.012 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 1.904 Fit side-chains REVERT: A 373 LYS cc_start: 0.6919 (mmtt) cc_final: 0.6658 (mmtt) REVERT: E 116 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8194 (mmm) outliers start: 30 outliers final: 8 residues processed: 96 average time/residue: 1.4591 time to fit residues: 157.1921 Evaluate side-chains 85 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 78 optimal weight: 0.3980 chunk 163 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN B 276 GLN D 310 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 17435 Z= 0.195 Angle : 0.505 15.426 23781 Z= 0.251 Chirality : 0.042 0.183 2815 Planarity : 0.003 0.035 2873 Dihedral : 9.046 123.023 3031 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.50 % Allowed : 7.35 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.21 (0.19), residues: 1995 helix: 2.73 (0.18), residues: 778 sheet: -0.68 (0.24), residues: 397 loop : -0.28 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 311 HIS 0.004 0.000 HIS B 60 PHE 0.011 0.001 PHE E 467 TYR 0.012 0.001 TYR B 439 ARG 0.004 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 1.966 Fit side-chains revert: symmetry clash REVERT: A 373 LYS cc_start: 0.6822 (mmtt) cc_final: 0.6562 (mmtt) REVERT: E 116 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8192 (mmm) outliers start: 28 outliers final: 12 residues processed: 98 average time/residue: 1.4218 time to fit residues: 156.2957 Evaluate side-chains 90 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 191 optimal weight: 0.0370 chunk 159 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS B 276 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 17435 Z= 0.243 Angle : 0.512 16.257 23781 Z= 0.255 Chirality : 0.042 0.186 2815 Planarity : 0.003 0.044 2873 Dihedral : 8.846 122.509 3031 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.34 % Allowed : 7.89 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.22 (0.19), residues: 1995 helix: 2.74 (0.18), residues: 777 sheet: -0.69 (0.24), residues: 401 loop : -0.26 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 311 HIS 0.005 0.001 HIS E 315 PHE 0.012 0.001 PHE E 467 TYR 0.013 0.001 TYR B 439 ARG 0.010 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 1.785 Fit side-chains revert: symmetry clash REVERT: A 282 MET cc_start: 0.7989 (ttm) cc_final: 0.7725 (mtp) REVERT: A 373 LYS cc_start: 0.6940 (mmtt) cc_final: 0.6601 (mmtt) REVERT: D 407 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7995 (m-30) REVERT: E 116 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8151 (mmm) outliers start: 25 outliers final: 12 residues processed: 93 average time/residue: 1.4919 time to fit residues: 155.0896 Evaluate side-chains 89 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 161 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 190 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN D 310 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 17435 Z= 0.184 Angle : 0.498 16.482 23781 Z= 0.248 Chirality : 0.042 0.172 2815 Planarity : 0.003 0.036 2873 Dihedral : 8.446 120.677 3031 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.23 % Allowed : 8.21 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.27 (0.19), residues: 1995 helix: 2.79 (0.18), residues: 778 sheet: -0.70 (0.24), residues: 395 loop : -0.23 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 311 HIS 0.004 0.000 HIS D 408 PHE 0.012 0.001 PHE E 467 TYR 0.011 0.001 TYR B 439 ARG 0.004 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 282 MET cc_start: 0.8006 (ttm) cc_final: 0.7755 (mtp) REVERT: A 373 LYS cc_start: 0.6807 (mmtt) cc_final: 0.6509 (mmtt) REVERT: A 416 LEU cc_start: 0.8754 (tt) cc_final: 0.8433 (mp) REVERT: E 116 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8162 (mmm) outliers start: 23 outliers final: 9 residues processed: 96 average time/residue: 1.5581 time to fit residues: 166.1982 Evaluate side-chains 87 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 57 optimal weight: 0.0040 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN B 276 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 17435 Z= 0.178 Angle : 0.493 16.912 23781 Z= 0.246 Chirality : 0.042 0.167 2815 Planarity : 0.003 0.036 2873 Dihedral : 8.263 119.775 3031 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.97 % Allowed : 8.96 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.30 (0.19), residues: 1995 helix: 2.83 (0.18), residues: 778 sheet: -0.68 (0.24), residues: 394 loop : -0.22 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 311 HIS 0.003 0.001 HIS B 60 PHE 0.012 0.001 PHE E 467 TYR 0.012 0.001 TYR B 439 ARG 0.004 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.6689 (t0) cc_final: 0.6272 (t0) REVERT: A 282 MET cc_start: 0.8004 (ttm) cc_final: 0.7753 (mtp) REVERT: A 373 LYS cc_start: 0.6717 (mmtt) cc_final: 0.6429 (mmtt) REVERT: A 416 LEU cc_start: 0.8747 (tt) cc_final: 0.8430 (mp) REVERT: E 116 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8142 (mmm) outliers start: 18 outliers final: 13 residues processed: 92 average time/residue: 1.4960 time to fit residues: 153.6218 Evaluate side-chains 91 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 chunk 107 optimal weight: 0.0170 chunk 77 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN D 310 GLN D 322 ASN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 17435 Z= 0.171 Angle : 0.489 17.124 23781 Z= 0.244 Chirality : 0.041 0.158 2815 Planarity : 0.003 0.037 2873 Dihedral : 8.062 118.161 3031 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.86 % Allowed : 9.23 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.34 (0.19), residues: 1995 helix: 2.86 (0.18), residues: 778 sheet: -0.66 (0.24), residues: 394 loop : -0.20 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 311 HIS 0.013 0.001 HIS E 323 PHE 0.022 0.001 PHE C 468 TYR 0.011 0.001 TYR B 439 ARG 0.004 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.6659 (t0) cc_final: 0.6242 (t0) REVERT: A 282 MET cc_start: 0.8012 (ttm) cc_final: 0.7762 (mtp) REVERT: A 373 LYS cc_start: 0.6689 (mmtt) cc_final: 0.6421 (mmtt) REVERT: E 116 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8097 (mmm) outliers start: 16 outliers final: 12 residues processed: 90 average time/residue: 1.5415 time to fit residues: 154.3490 Evaluate side-chains 90 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 130 optimal weight: 0.0570 chunk 197 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 16 optimal weight: 0.0970 chunk 121 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS B 276 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 17435 Z= 0.205 Angle : 0.505 17.564 23781 Z= 0.251 Chirality : 0.042 0.162 2815 Planarity : 0.003 0.036 2873 Dihedral : 7.966 117.293 3031 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.81 % Allowed : 9.61 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.19), residues: 1995 helix: 2.87 (0.18), residues: 778 sheet: -0.65 (0.24), residues: 394 loop : -0.19 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 311 HIS 0.007 0.001 HIS E 323 PHE 0.012 0.001 PHE E 467 TYR 0.012 0.001 TYR B 439 ARG 0.003 0.000 ARG C 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.6738 (t0) cc_final: 0.6313 (t0) REVERT: A 282 MET cc_start: 0.8003 (ttm) cc_final: 0.7765 (mtp) REVERT: A 373 LYS cc_start: 0.6698 (mmtt) cc_final: 0.6421 (mmtt) REVERT: E 116 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8132 (mmm) outliers start: 15 outliers final: 12 residues processed: 89 average time/residue: 1.4975 time to fit residues: 148.7497 Evaluate side-chains 90 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 23 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS B 95 GLN B 276 GLN D 310 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.065453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.050057 restraints weight = 39349.318| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 2.79 r_work: 0.2595 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 17435 Z= 0.228 Angle : 0.511 17.783 23781 Z= 0.254 Chirality : 0.042 0.166 2815 Planarity : 0.003 0.036 2873 Dihedral : 7.887 116.168 3031 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.81 % Allowed : 9.66 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.39 (0.19), residues: 1995 helix: 2.88 (0.18), residues: 777 sheet: -0.66 (0.24), residues: 393 loop : -0.14 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 311 HIS 0.006 0.001 HIS E 323 PHE 0.035 0.001 PHE C 468 TYR 0.012 0.001 TYR B 439 ARG 0.003 0.000 ARG C 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4042.28 seconds wall clock time: 74 minutes 44.13 seconds (4484.13 seconds total)