Starting phenix.real_space_refine on Sun Dec 10 19:16:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qne_14076/12_2023/7qne_14076_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qne_14076/12_2023/7qne_14076.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qne_14076/12_2023/7qne_14076_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qne_14076/12_2023/7qne_14076_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qne_14076/12_2023/7qne_14076_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qne_14076/12_2023/7qne_14076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qne_14076/12_2023/7qne_14076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qne_14076/12_2023/7qne_14076_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qne_14076/12_2023/7qne_14076_updated.pdb" } 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 82 5.16 5 Cl 3 4.86 5 C 9908 2.51 5 N 2482 2.21 5 O 2821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15302 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2801 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 345, 2793 Classifications: {'peptide': 345} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 330} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 345, 2793 Classifications: {'peptide': 345} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 330} Chain breaks: 1 bond proxies already assigned to first conformer: 2855 Chain: "B" Number of atoms: 2751 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2742 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 334, 2742 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain breaks: 1 bond proxies already assigned to first conformer: 2804 Chain: "C" Number of atoms: 2712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2712 Classifications: {'peptide': 329} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 315} Chain breaks: 1 Chain: "D" Number of atoms: 2795 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 343, 2780 Classifications: {'peptide': 343} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 328} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 343, 2780 Classifications: {'peptide': 343} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 328} Chain breaks: 1 bond proxies already assigned to first conformer: 2833 Chain: "E" Number of atoms: 2745 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2740 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 334, 2740 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain breaks: 1 bond proxies already assigned to first conformer: 2807 Chain: "G" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 949 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "a" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 9 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 6 Chain: "d" 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: 6 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 66 Unusual residues: {' CL': 1, 'D10': 1, 'OCT': 1, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'D10': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' CL': 1, 'D10': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {' CL': 1, 'EIE': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'D10': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.68, per 1000 atoms: 0.83 Number of scatterers: 15302 At special positions: 0 Unit cell: (103.936, 102.144, 136.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 3 17.00 S 82 16.00 P 6 15.00 O 2821 8.00 N 2482 7.00 C 9908 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " 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 ALPHA1-2 " MAN a 4 " - " MAN a 5 " " MAN a 5 " - " MAN a 6 " ALPHA1-3 " BMA F 3 " - " MAN F 6 " " MAN F 4 " - " MAN F 5 " " BMA H 3 " - " MAN H 6 " " MAN H 4 " - " MAN H 5 " " BMA a 3 " - " MAN a 4 " " MAN a 7 " - " MAN a 8 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA a 3 " - " MAN a 7 " " MAN a 7 " - " MAN a 9 " " BMA d 3 " - " MAN d 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG C 503 " - " ASN C 208 " " NAG F 1 " - " ASN B 149 " " NAG H 1 " - " ASN E 149 " " NAG a 1 " - " ASN A 111 " " NAG b 1 " - " ASN B 80 " " NAG d 1 " - " ASN D 111 " " NAG e 1 " - " ASN E 80 " Time building additional restraints: 6.53 Conformation dependent library (CDL) restraints added in 4.3 seconds 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 20 sheets defined 33.8% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 88 through 93 removed outlier: 3.745A pdb=" N LYS A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 175 through 178 No H-bonds generated for 'chain 'A' and resid 175 through 178' Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 231 through 246 removed outlier: 3.768A pdb=" N SER A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TRP A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 276 removed outlier: 3.501A pdb=" N ASN A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 310 removed outlier: 3.614A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 417 removed outlier: 3.944A pdb=" N ILE A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Proline residue: A 401 - end of helix Processing helix chain 'B' and resid 11 through 20 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.691A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 241 removed outlier: 3.521A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 271 removed outlier: 3.582A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 307 removed outlier: 3.741A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 446 removed outlier: 3.549A pdb=" N ASP B 424 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 27 through 35 Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 234 through 239 removed outlier: 3.524A pdb=" N ILE C 238 " --> pdb=" O GLY C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 256 removed outlier: 3.739A pdb=" N VAL C 253 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TRP C 256 " --> pdb=" O TRP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 281 removed outlier: 3.516A pdb=" N THR C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 321 Processing helix chain 'C' and resid 407 through 434 removed outlier: 4.827A pdb=" N ASP C 411 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE C 417 " --> pdb=" O ALA C 414 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N PHE C 418 " --> pdb=" O ARG C 415 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.666A pdb=" N PHE C 422 " --> pdb=" O PRO C 419 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 424 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C 429 " --> pdb=" O ASN C 426 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP C 430 " --> pdb=" O LEU C 427 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL C 431 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 432 " --> pdb=" O TYR C 429 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR C 433 " --> pdb=" O TRP C 430 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C 434 " --> pdb=" O VAL C 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 20 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 88 through 93 removed outlier: 3.888A pdb=" N LYS D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 175 through 178 No H-bonds generated for 'chain 'D' and resid 175 through 178' Processing helix chain 'D' and resid 224 through 229 removed outlier: 3.511A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 246 removed outlier: 3.883A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TRP D 246 " --> pdb=" O GLN D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 276 removed outlier: 3.564A pdb=" N THR D 262 " --> pdb=" O PHE D 258 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 310 removed outlier: 3.591A pdb=" N LEU D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE D 310 " --> pdb=" O THR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 415 removed outlier: 3.688A pdb=" N ILE D 398 " --> pdb=" O ARG D 394 " (cutoff:3.500A) Proline residue: D 401 - end of helix Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 85 through 90 Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 219 through 224 removed outlier: 3.560A pdb=" N LEU E 223 " --> pdb=" O GLY E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 241 removed outlier: 3.656A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N PHE E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP E 241 " --> pdb=" O TRP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 271 removed outlier: 3.544A pdb=" N GLU E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 307 removed outlier: 3.549A pdb=" N ALA E 300 " --> pdb=" O LEU E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 446 removed outlier: 3.781A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Proline residue: E 432 - end of helix Processing helix chain 'G' and resid 87 through 89 No H-bonds generated for 'chain 'G' and resid 87 through 89' Processing helix chain 'G' and resid 107 through 109 No H-bonds generated for 'chain 'G' and resid 107 through 109' Processing sheet with id= A, first strand: chain 'A' and resid 167 through 171 removed outlier: 6.268A pdb=" N THR A 39 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLU A 170 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL A 41 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU A 40 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS A 71 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASP A 63 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N PHE A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR A 61 " --> pdb=" O PHE A 50 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.298A pdb=" N SER A 159 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL A 211 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY A 195 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LYS A 220 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU A 193 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 164 through 168 removed outlier: 6.394A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.969A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.668A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 179 through 183 removed outlier: 6.056A pdb=" N THR C 51 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLN C 182 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE C 53 " --> pdb=" O GLN C 182 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU C 52 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASP C 75 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 57 through 59 Processing sheet with id= I, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.609A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY C 205 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER C 230 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N PHE C 203 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 116 through 121 removed outlier: 6.692A pdb=" N ASP C 148 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA C 119 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR C 146 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 167 through 171 removed outlier: 6.220A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE D 46 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 45 through 47 Processing sheet with id= M, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= N, first strand: chain 'D' and resid 196 through 205 Processing sheet with id= O, first strand: chain 'E' and resid 164 through 168 removed outlier: 6.312A pdb=" N VAL E 36 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N TYR E 167 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL E 38 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.060A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.775A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 3 through 7 Processing sheet with id= S, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.655A pdb=" N THR G 120 " --> pdb=" O VAL G 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'G' and resid 117 through 119 removed outlier: 5.970A pdb=" N ARG G 38 " --> pdb=" O PHE G 47 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N PHE G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1838 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: 4.77 Time building geometry restraints manager: 7.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 2275 1.27 - 1.41: 4213 1.41 - 1.54: 9010 1.54 - 1.68: 47 1.68 - 1.81: 141 Bond restraints: 15686 Sorted by residual: bond pdb=" C1B PIO A 501 " pdb=" O3C PIO A 501 " ideal model delta sigma weight residual 1.399 1.333 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C1B PIO D 503 " pdb=" O3C PIO D 503 " ideal model delta sigma weight residual 1.399 1.334 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C2C PIO D 503 " pdb=" O2C PIO D 503 " ideal model delta sigma weight residual 1.399 1.461 -0.062 2.00e-02 2.50e+03 9.69e+00 bond pdb=" C2C PIO A 501 " pdb=" O2C PIO A 501 " ideal model delta sigma weight residual 1.399 1.461 -0.062 2.00e-02 2.50e+03 9.53e+00 bond pdb=" C1A PIO A 501 " pdb=" O2C PIO A 501 " ideal model delta sigma weight residual 1.399 1.340 0.059 2.00e-02 2.50e+03 8.56e+00 ... (remaining 15681 not shown) Histogram of bond angle deviations from ideal: 99.63 - 113.44: 9144 113.44 - 127.25: 11992 127.25 - 141.06: 173 141.06 - 154.88: 0 154.88 - 168.69: 1 Bond angle restraints: 21310 Sorted by residual: angle pdb=" C4 PIO D 503 " pdb=" O4 PIO D 503 " pdb=" P4 PIO D 503 " ideal model delta sigma weight residual 118.46 132.46 -14.00 3.00e+00 1.11e-01 2.18e+01 angle pdb=" C4 PIO A 501 " pdb=" O4 PIO A 501 " pdb=" P4 PIO A 501 " ideal model delta sigma weight residual 118.46 132.33 -13.87 3.00e+00 1.11e-01 2.14e+01 angle pdb=" C2A PIO D 503 " pdb=" C1A PIO D 503 " pdb=" O2C PIO D 503 " ideal model delta sigma weight residual 120.00 111.08 8.92 3.00e+00 1.11e-01 8.83e+00 angle pdb=" C2A PIO A 501 " pdb=" C1A PIO A 501 " pdb=" O2C PIO A 501 " ideal model delta sigma weight residual 120.00 111.12 8.88 3.00e+00 1.11e-01 8.77e+00 angle pdb=" C5 PIO A 501 " pdb=" O5 PIO A 501 " pdb=" P5 PIO A 501 " ideal model delta sigma weight residual 118.46 127.24 -8.78 3.00e+00 1.11e-01 8.56e+00 ... (remaining 21305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 8871 16.88 - 33.76: 317 33.76 - 50.64: 51 50.64 - 67.52: 14 67.52 - 84.40: 4 Dihedral angle restraints: 9257 sinusoidal: 3915 harmonic: 5342 Sorted by residual: dihedral pdb=" CA ILE C 76 " pdb=" C ILE C 76 " pdb=" N PHE C 77 " pdb=" CA PHE C 77 " ideal model delta harmonic sigma weight residual 180.00 158.78 21.22 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA GLY B 170 " pdb=" C GLY B 170 " pdb=" N GLY B 171 " pdb=" CA GLY B 171 " ideal model delta harmonic sigma weight residual -180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA VAL A 64 " pdb=" C VAL A 64 " pdb=" N PHE A 65 " pdb=" CA PHE A 65 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 9254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2147 0.059 - 0.118: 297 0.118 - 0.177: 20 0.177 - 0.237: 5 0.237 - 0.296: 6 Chirality restraints: 2475 Sorted by residual: chirality pdb=" C1 BMA d 3 " pdb=" O4 NAG d 2 " pdb=" C2 BMA d 3 " pdb=" O5 BMA d 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.16e+02 chirality pdb=" C1 MAN a 4 " pdb=" O3 BMA a 3 " pdb=" C2 MAN a 4 " pdb=" O5 MAN a 4 " both_signs ideal model delta sigma weight residual False 2.40 2.17 0.23 2.00e-02 2.50e+03 1.28e+02 chirality pdb=" C1 MAN a 7 " pdb=" O6 BMA a 3 " pdb=" C2 MAN a 7 " pdb=" O5 MAN a 7 " both_signs ideal model delta sigma weight residual False 2.40 2.17 0.23 2.00e-02 2.50e+03 1.27e+02 ... (remaining 2472 not shown) Planarity restraints: 2592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 EIE D 502 " -0.145 2.00e-02 2.50e+03 1.47e-01 5.91e+02 pdb=" C11 EIE D 502 " -0.150 2.00e-02 2.50e+03 pdb=" C12 EIE D 502 " -0.072 2.00e-02 2.50e+03 pdb=" C13 EIE D 502 " 0.016 2.00e-02 2.50e+03 pdb=" C7 EIE D 502 " 0.170 2.00e-02 2.50e+03 pdb=" C8 EIE D 502 " 0.031 2.00e-02 2.50e+03 pdb=" C9 EIE D 502 " -0.055 2.00e-02 2.50e+03 pdb=" N1 EIE D 502 " -0.236 2.00e-02 2.50e+03 pdb=" N2 EIE D 502 " 0.068 2.00e-02 2.50e+03 pdb=" N3 EIE D 502 " 0.298 2.00e-02 2.50e+03 pdb=" N4 EIE D 502 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.031 2.00e-02 2.50e+03 2.54e-02 8.04e+00 pdb=" C7 NAG F 1 " 0.010 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.024 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.040 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.018 2.00e-02 2.50e+03 1.46e-02 2.67e+00 pdb=" C7 NAG H 1 " 0.007 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.014 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.022 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.002 2.00e-02 2.50e+03 ... (remaining 2589 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2569 2.77 - 3.30: 14062 3.30 - 3.83: 26383 3.83 - 4.37: 32837 4.37 - 4.90: 54874 Nonbonded interactions: 130725 Sorted by model distance: nonbonded pdb=" O VAL A 257 " pdb=" OG1 THR A 261 " model vdw 2.237 2.440 nonbonded pdb=" ND2AASN E 41 " pdb=" O ARG E 169 " model vdw 2.287 2.520 nonbonded pdb=" OE1 GLU E 153 " pdb=" OG SER E 209 " model vdw 2.290 2.440 nonbonded pdb=" OG1 THR A 267 " pdb=" OH TYR A 294 " model vdw 2.297 2.440 nonbonded pdb=" O SER A 92 " pdb=" NH1 ARG E 86 " model vdw 2.304 2.520 ... (remaining 130720 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' and (resid 13 through 66 or resid 68 through 101 or resid 103 through \ 320 or resid 384 through 418)) selection = (chain 'D' and (resid 13 through 66 or resid 68 through 101 or resid 103 through \ 418)) } ncs_group { reference = (chain 'B' and (resid 10 through 40 or resid 42 through 65 or resid 67 through 3 \ 12 or resid 419 through 447 or resid 3101)) selection = (chain 'E' and (resid 10 through 40 or resid 42 through 65 or resid 67 through 4 \ 47 or resid 3201)) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'b' selection = chain 'e' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=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: 1.180 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: 5.750 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 50.470 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 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 : 0.004 0.066 15686 Z= 0.257 Angle : 0.596 14.000 21310 Z= 0.257 Chirality : 0.044 0.296 2475 Planarity : 0.004 0.147 2585 Dihedral : 9.345 84.400 5812 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.25 % Allowed : 2.79 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: 0.58 (0.20), residues: 1791 helix: 0.88 (0.21), residues: 559 sheet: 0.32 (0.23), residues: 482 loop : 0.23 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 426 HIS 0.003 0.001 HIS B 267 PHE 0.010 0.001 PHE C 113 TYR 0.013 0.001 TYR B 277 ARG 0.003 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 421 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 424 average time/residue: 1.4249 time to fit residues: 657.7277 Evaluate side-chains 299 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 297 time to evaluate : 1.788 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 0.1874 time to fit residues: 2.6411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 229 GLN B 265 ASN B 421 ASN C 60 ASN C 80 GLN C 182 GLN C 426 ASN D 68 GLN D 116 ASN D 190 GLN D 229 GLN D 408 ASN E 119 HIS E 243 ASN E 265 ASN E 312 GLN G 81 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15686 Z= 0.218 Angle : 0.543 9.133 21310 Z= 0.282 Chirality : 0.042 0.182 2475 Planarity : 0.004 0.045 2585 Dihedral : 5.850 71.439 2412 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.91 % Allowed : 12.02 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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 (0.20), residues: 1791 helix: 1.75 (0.21), residues: 561 sheet: 0.21 (0.23), residues: 482 loop : 0.25 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 317 HIS 0.004 0.001 HIS D 110 PHE 0.014 0.001 PHE A 304 TYR 0.025 0.002 TYR E 299 ARG 0.009 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 298 time to evaluate : 1.975 Fit side-chains revert: symmetry clash outliers start: 47 outliers final: 14 residues processed: 312 average time/residue: 1.3671 time to fit residues: 467.6702 Evaluate side-chains 299 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 285 time to evaluate : 1.756 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 7 residues processed: 8 average time/residue: 0.5287 time to fit residues: 7.8217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 174 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 160 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 242 GLN A 275 ASN B 265 ASN C 182 GLN D 87 ASN D 204 GLN D 387 ASN D 408 ASN E 265 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15686 Z= 0.183 Angle : 0.503 6.727 21310 Z= 0.261 Chirality : 0.041 0.178 2475 Planarity : 0.004 0.035 2585 Dihedral : 5.734 72.171 2412 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.42 % Allowed : 13.51 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: 1.12 (0.20), residues: 1791 helix: 2.03 (0.21), residues: 558 sheet: 0.24 (0.23), residues: 478 loop : 0.23 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 317 HIS 0.003 0.001 HIS D 110 PHE 0.014 0.001 PHE A 304 TYR 0.027 0.001 TYR E 299 ARG 0.009 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 297 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 15 residues processed: 312 average time/residue: 1.4090 time to fit residues: 481.0750 Evaluate side-chains 299 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 284 time to evaluate : 1.922 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 8 residues processed: 8 average time/residue: 0.6401 time to fit residues: 8.6891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 242 GLN A 275 ASN B 265 ASN B 421 ASN C 182 GLN E 265 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15686 Z= 0.270 Angle : 0.560 9.091 21310 Z= 0.288 Chirality : 0.043 0.189 2475 Planarity : 0.004 0.038 2585 Dihedral : 6.039 74.164 2412 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.04 % Allowed : 13.32 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: 1.05 (0.20), residues: 1791 helix: 2.02 (0.22), residues: 556 sheet: 0.21 (0.23), residues: 461 loop : 0.13 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 317 HIS 0.004 0.001 HIS A 218 PHE 0.018 0.002 PHE A 304 TYR 0.030 0.002 TYR E 299 ARG 0.007 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 284 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 22 residues processed: 308 average time/residue: 1.4195 time to fit residues: 478.2011 Evaluate side-chains 309 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 287 time to evaluate : 1.754 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 13 residues processed: 10 average time/residue: 0.6495 time to fit residues: 10.1341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 146 optimal weight: 0.0060 chunk 118 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 242 GLN A 275 ASN B 265 ASN B 421 ASN C 182 GLN E 265 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15686 Z= 0.170 Angle : 0.496 7.484 21310 Z= 0.256 Chirality : 0.041 0.178 2475 Planarity : 0.004 0.055 2585 Dihedral : 5.789 73.676 2412 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.29 % Allowed : 14.19 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: 1.15 (0.20), residues: 1791 helix: 2.12 (0.22), residues: 557 sheet: 0.23 (0.23), residues: 480 loop : 0.20 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 317 HIS 0.003 0.001 HIS D 110 PHE 0.013 0.001 PHE A 304 TYR 0.029 0.001 TYR E 299 ARG 0.007 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 295 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 19 residues processed: 312 average time/residue: 1.4205 time to fit residues: 484.3128 Evaluate side-chains 300 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 281 time to evaluate : 1.862 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 6 average time/residue: 0.3670 time to fit residues: 5.2717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 172 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 166 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN B 265 ASN C 182 GLN D 87 ASN D 387 ASN E 265 ASN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15686 Z= 0.278 Angle : 0.558 8.933 21310 Z= 0.286 Chirality : 0.043 0.185 2475 Planarity : 0.004 0.075 2585 Dihedral : 6.064 75.147 2412 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.91 % Allowed : 14.06 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: 1.05 (0.20), residues: 1791 helix: 2.01 (0.22), residues: 556 sheet: 0.18 (0.22), residues: 480 loop : 0.17 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 317 HIS 0.005 0.001 HIS A 218 PHE 0.019 0.002 PHE A 304 TYR 0.031 0.002 TYR E 299 ARG 0.011 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 283 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 23 residues processed: 305 average time/residue: 1.4765 time to fit residues: 491.8683 Evaluate side-chains 304 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 281 time to evaluate : 1.814 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 15 residues processed: 10 average time/residue: 0.7886 time to fit residues: 11.6271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 144 optimal weight: 0.1980 chunk 96 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN B 265 ASN B 421 ASN C 182 GLN E 265 ASN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15686 Z= 0.168 Angle : 0.495 7.973 21310 Z= 0.256 Chirality : 0.041 0.172 2475 Planarity : 0.004 0.050 2585 Dihedral : 5.774 74.148 2412 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.11 % Allowed : 15.43 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: 1.18 (0.20), residues: 1791 helix: 2.10 (0.22), residues: 560 sheet: 0.27 (0.23), residues: 474 loop : 0.23 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 426 HIS 0.003 0.001 HIS D 110 PHE 0.014 0.001 PHE A 298 TYR 0.029 0.001 TYR E 299 ARG 0.006 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 284 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 23 residues processed: 303 average time/residue: 1.4390 time to fit residues: 477.6909 Evaluate side-chains 298 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 275 time to evaluate : 1.843 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 17 residues processed: 8 average time/residue: 0.5272 time to fit residues: 7.9693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN B 265 ASN C 182 GLN E 265 ASN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15686 Z= 0.272 Angle : 0.549 8.113 21310 Z= 0.283 Chirality : 0.043 0.179 2475 Planarity : 0.004 0.050 2585 Dihedral : 5.955 75.168 2412 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.11 % Allowed : 15.92 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: 1.04 (0.20), residues: 1791 helix: 1.98 (0.22), residues: 558 sheet: 0.16 (0.22), residues: 482 loop : 0.19 (0.24), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 183 HIS 0.005 0.001 HIS A 218 PHE 0.019 0.002 PHE A 304 TYR 0.031 0.002 TYR E 299 ARG 0.008 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 281 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 20 residues processed: 298 average time/residue: 1.4708 time to fit residues: 478.6547 Evaluate side-chains 298 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 278 time to evaluate : 1.657 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 6 average time/residue: 0.5524 time to fit residues: 6.3116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 4.9990 chunk 159 optimal weight: 0.0970 chunk 164 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 125 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN B 265 ASN B 421 ASN C 182 GLN E 265 ASN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15686 Z= 0.188 Angle : 0.507 8.021 21310 Z= 0.262 Chirality : 0.041 0.167 2475 Planarity : 0.004 0.042 2585 Dihedral : 5.765 74.068 2412 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.92 % Allowed : 16.29 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: 1.15 (0.20), residues: 1791 helix: 2.07 (0.22), residues: 559 sheet: 0.26 (0.23), residues: 474 loop : 0.23 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 317 HIS 0.004 0.001 HIS D 110 PHE 0.015 0.001 PHE A 298 TYR 0.030 0.001 TYR E 299 ARG 0.005 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 287 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 20 residues processed: 304 average time/residue: 1.4378 time to fit residues: 479.0082 Evaluate side-chains 301 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 281 time to evaluate : 1.758 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 6 average time/residue: 0.9648 time to fit residues: 8.6557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.0980 chunk 80 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 112 optimal weight: 0.0970 chunk 150 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN B 265 ASN C 182 GLN D 189 ASN E 265 ASN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15686 Z= 0.158 Angle : 0.498 7.931 21310 Z= 0.258 Chirality : 0.041 0.161 2475 Planarity : 0.004 0.047 2585 Dihedral : 5.636 73.143 2412 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.24 % Allowed : 17.04 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: 1.20 (0.20), residues: 1791 helix: 2.14 (0.22), residues: 557 sheet: 0.26 (0.23), residues: 476 loop : 0.26 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 183 HIS 0.003 0.001 HIS D 110 PHE 0.014 0.001 PHE A 298 TYR 0.029 0.001 TYR E 299 ARG 0.006 0.000 ARG B 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 289 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 303 average time/residue: 1.5513 time to fit residues: 512.2850 Evaluate side-chains 293 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 278 time to evaluate : 2.328 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.2264 time to fit residues: 3.0328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 145 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN B 265 ASN C 182 GLN D 87 ASN D 189 ASN E 265 ASN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.124638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.096089 restraints weight = 25489.629| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.27 r_work: 0.2883 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15686 Z= 0.239 Angle : 0.538 7.938 21310 Z= 0.278 Chirality : 0.042 0.169 2475 Planarity : 0.004 0.043 2585 Dihedral : 5.806 73.546 2412 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.55 % Allowed : 16.85 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: 1.13 (0.20), residues: 1791 helix: 2.01 (0.22), residues: 560 sheet: 0.22 (0.23), residues: 476 loop : 0.26 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 183 HIS 0.004 0.001 HIS A 218 PHE 0.018 0.002 PHE C 236 TYR 0.030 0.002 TYR E 299 ARG 0.008 0.000 ARG B 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7618.82 seconds wall clock time: 135 minutes 18.99 seconds (8118.99 seconds total)