Starting phenix.real_space_refine on Sat Jun 14 02:37:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wz3_37945/06_2025/8wz3_37945.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wz3_37945/06_2025/8wz3_37945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wz3_37945/06_2025/8wz3_37945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wz3_37945/06_2025/8wz3_37945.map" model { file = "/net/cci-nas-00/data/ceres_data/8wz3_37945/06_2025/8wz3_37945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wz3_37945/06_2025/8wz3_37945.cif" } resolution = 3.19 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= 0.020 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 9987 2.51 5 N 2577 2.21 5 O 3087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15741 Number of models: 1 Model: "" Number of chains: 4 Chain: "F" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "A" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3477 Classifications: {'peptide': 449} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 436} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 925 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, D, G, H, K Time building chain proxies: 10.25, per 1000 atoms: 0.65 Number of scatterers: 15741 At special positions: 0 Unit cell: (138.484, 150.154, 123.702, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3087 8.00 N 2577 7.00 C 9987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 NAG-ASN " NAG A 601 " - " ASN A 500 " " NAG B 601 " - " ASN B 500 " " NAG C 601 " - " ASN C 500 " Time building additional restraints: 3.94 Conformation dependent library (CDL) restraints added in 2.1 seconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3762 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 36 sheets defined 25.4% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'D' and resid 62 through 65 removed outlier: 4.184A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.954A pdb=" N THR D 91 " --> pdb=" O ASN D 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 98 Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.859A pdb=" N LEU A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 142 " --> pdb=" O GLY A 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 138 through 142' Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 195 through 209 Proline residue: A 205 - end of helix Processing helix chain 'A' and resid 217 through 241 removed outlier: 3.805A pdb=" N ILE A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 262 Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 277 through 283 Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.750A pdb=" N SER A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 385 Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 491 through 512 Processing helix chain 'E' and resid 62 through 65 removed outlier: 4.184A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.955A pdb=" N THR E 91 " --> pdb=" O ASN E 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 98 Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.859A pdb=" N LEU B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU B 142 " --> pdb=" O GLY B 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 138 through 142' Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 195 through 209 Proline residue: B 205 - end of helix Processing helix chain 'B' and resid 217 through 241 removed outlier: 3.805A pdb=" N ILE B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 262 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.750A pdb=" N SER B 372 " --> pdb=" O THR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 385 Processing helix chain 'B' and resid 473 through 477 Processing helix chain 'B' and resid 491 through 512 Processing helix chain 'G' and resid 62 through 65 removed outlier: 4.184A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.955A pdb=" N THR G 91 " --> pdb=" O ASN G 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 98 Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.859A pdb=" N LEU C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU C 142 " --> pdb=" O GLY C 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 138 through 142' Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 195 through 209 Proline residue: C 205 - end of helix Processing helix chain 'C' and resid 217 through 241 removed outlier: 3.805A pdb=" N ILE C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 262 Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 277 through 283 Processing helix chain 'C' and resid 368 through 372 removed outlier: 3.750A pdb=" N SER C 372 " --> pdb=" O THR C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 385 Processing helix chain 'C' and resid 473 through 477 Processing helix chain 'C' and resid 491 through 512 Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.509A pdb=" N VAL D 18 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.634A pdb=" N THR D 113 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR D 110 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR D 94 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 93 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.634A pdb=" N THR D 113 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR D 110 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR D 94 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG D 98 " --> pdb=" O TYR D 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.794A pdb=" N GLN F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 12 through 13 Processing sheet with id=AA6, first strand: chain 'F' and resid 45 through 46 Processing sheet with id=AA7, first strand: chain 'A' and resid 373 through 375 removed outlier: 3.663A pdb=" N TRP A 341 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU A 30 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL A 469 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE A 32 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 179 through 180 removed outlier: 10.336A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 192 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA A 47 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE A 309 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N ARG A 49 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY A 307 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 301 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA A 298 " --> pdb=" O CYS A 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 179 through 180 removed outlier: 10.336A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 192 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 333 through 336 removed outlier: 3.894A pdb=" N SER A 398 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 404 through 407 removed outlier: 3.536A pdb=" N CYS A 416 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 431 through 434 Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.509A pdb=" N VAL E 18 " --> pdb=" O ILE E 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.633A pdb=" N THR E 113 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR E 110 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR E 94 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E 93 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.633A pdb=" N THR E 113 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR E 110 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR E 94 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG E 98 " --> pdb=" O TYR E 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.793A pdb=" N GLN H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 12 through 13 Processing sheet with id=AB9, first strand: chain 'H' and resid 45 through 46 Processing sheet with id=AC1, first strand: chain 'B' and resid 373 through 375 removed outlier: 3.663A pdb=" N TRP B 341 " --> pdb=" O PHE B 352 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU B 30 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL B 469 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE B 32 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 179 through 180 removed outlier: 10.336A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 192 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA B 47 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE B 309 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N ARG B 49 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY B 307 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 301 " --> pdb=" O SER B 55 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA B 298 " --> pdb=" O CYS B 290 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 179 through 180 removed outlier: 10.336A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 192 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 333 through 336 removed outlier: 3.895A pdb=" N SER B 398 " --> pdb=" O CYS B 333 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 404 through 407 removed outlier: 3.536A pdb=" N CYS B 416 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 431 through 434 Processing sheet with id=AC7, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.509A pdb=" N VAL G 18 " --> pdb=" O ILE G 83 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.633A pdb=" N THR G 113 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR G 110 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR G 94 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE G 93 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.633A pdb=" N THR G 113 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR G 110 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR G 94 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG G 98 " --> pdb=" O TYR G 105 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.794A pdb=" N GLN K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 12 through 13 Processing sheet with id=AD3, first strand: chain 'K' and resid 45 through 46 Processing sheet with id=AD4, first strand: chain 'C' and resid 373 through 375 removed outlier: 3.662A pdb=" N TRP C 341 " --> pdb=" O PHE C 352 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU C 30 " --> pdb=" O LEU C 467 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL C 469 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE C 32 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 179 through 180 removed outlier: 10.336A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 192 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA C 47 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE C 309 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N ARG C 49 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY C 307 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL C 301 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA C 298 " --> pdb=" O CYS C 290 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 179 through 180 removed outlier: 10.336A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 192 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 333 through 336 removed outlier: 3.894A pdb=" N SER C 398 " --> pdb=" O CYS C 333 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 404 through 407 removed outlier: 3.536A pdb=" N CYS C 416 " --> pdb=" O GLY C 438 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 431 through 434 684 hydrogen bonds defined for protein. 1764 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: 5.70 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2607 1.30 - 1.43: 4050 1.43 - 1.56: 9258 1.56 - 1.70: 0 1.70 - 1.83: 120 Bond restraints: 16035 Sorted by residual: bond pdb=" C PHE B 190 " pdb=" O PHE B 190 " ideal model delta sigma weight residual 1.234 1.165 0.069 1.29e-02 6.01e+03 2.89e+01 bond pdb=" C PHE A 190 " pdb=" O PHE A 190 " ideal model delta sigma weight residual 1.234 1.165 0.069 1.29e-02 6.01e+03 2.87e+01 bond pdb=" C PHE C 190 " pdb=" O PHE C 190 " ideal model delta sigma weight residual 1.234 1.166 0.069 1.29e-02 6.01e+03 2.85e+01 bond pdb=" C PHE C 190 " pdb=" N LYS C 191 " ideal model delta sigma weight residual 1.331 1.290 0.040 1.29e-02 6.01e+03 9.82e+00 bond pdb=" C PHE B 190 " pdb=" N LYS B 191 " ideal model delta sigma weight residual 1.331 1.290 0.040 1.29e-02 6.01e+03 9.77e+00 ... (remaining 16030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 20891 1.39 - 2.78: 693 2.78 - 4.16: 115 4.16 - 5.55: 24 5.55 - 6.94: 6 Bond angle restraints: 21729 Sorted by residual: angle pdb=" CA PHE A 190 " pdb=" C PHE A 190 " pdb=" O PHE A 190 " ideal model delta sigma weight residual 120.75 116.12 4.63 1.12e+00 7.97e-01 1.71e+01 angle pdb=" CA PHE B 190 " pdb=" C PHE B 190 " pdb=" O PHE B 190 " ideal model delta sigma weight residual 120.75 116.13 4.62 1.12e+00 7.97e-01 1.70e+01 angle pdb=" CA PHE C 190 " pdb=" C PHE C 190 " pdb=" O PHE C 190 " ideal model delta sigma weight residual 120.75 116.15 4.60 1.12e+00 7.97e-01 1.69e+01 angle pdb=" N GLN C 501 " pdb=" CA GLN C 501 " pdb=" C GLN C 501 " ideal model delta sigma weight residual 111.33 106.91 4.42 1.21e+00 6.83e-01 1.33e+01 angle pdb=" N GLN B 501 " pdb=" CA GLN B 501 " pdb=" C GLN B 501 " ideal model delta sigma weight residual 111.33 106.93 4.40 1.21e+00 6.83e-01 1.32e+01 ... (remaining 21724 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.41: 9031 23.41 - 46.83: 509 46.83 - 70.24: 54 70.24 - 93.66: 3 93.66 - 117.07: 51 Dihedral angle restraints: 9648 sinusoidal: 3789 harmonic: 5859 Sorted by residual: dihedral pdb=" C1 NAG A 601 " pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " pdb=" C4 NAG A 601 " ideal model delta sinusoidal sigma weight residual -64.11 52.96 -117.07 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" C1 NAG B 601 " pdb=" C5 NAG B 601 " pdb=" O5 NAG B 601 " pdb=" C4 NAG B 601 " ideal model delta sinusoidal sigma weight residual -64.11 52.96 -117.07 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" C2 NAG B 601 " pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " pdb=" C5 NAG B 601 " ideal model delta sinusoidal sigma weight residual -62.96 54.09 -117.05 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 9645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 2501 0.128 - 0.256: 13 0.256 - 0.385: 3 0.385 - 0.513: 0 0.513 - 0.641: 3 Chirality restraints: 2520 Sorted by residual: chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 500 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 500 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 500 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.02e+01 ... (remaining 2517 not shown) Planarity restraints: 2739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 200 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C ASP B 200 " 0.034 2.00e-02 2.50e+03 pdb=" O ASP B 200 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS B 201 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 200 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.75e+00 pdb=" C ASP C 200 " -0.033 2.00e-02 2.50e+03 pdb=" O ASP C 200 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS C 201 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 200 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C ASP A 200 " 0.033 2.00e-02 2.50e+03 pdb=" O ASP A 200 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 201 " -0.011 2.00e-02 2.50e+03 ... (remaining 2736 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 162 2.60 - 3.18: 13305 3.18 - 3.75: 22744 3.75 - 4.33: 33403 4.33 - 4.90: 57337 Nonbonded interactions: 126951 Sorted by model distance: nonbonded pdb=" SG CYS A 416 " pdb=" SG CYS A 422 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS B 416 " pdb=" SG CYS B 422 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS C 416 " pdb=" SG CYS C 422 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS A 69 " pdb=" SG CYS A 212 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS B 69 " pdb=" SG CYS B 212 " model vdw 2.029 3.760 ... (remaining 126946 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 18.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 37.940 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 0.069 16038 Z= 0.185 Angle : 0.606 6.942 21738 Z= 0.350 Chirality : 0.049 0.641 2520 Planarity : 0.004 0.046 2736 Dihedral : 16.998 117.069 5886 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.17 % Allowed : 5.35 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -4.35 (0.15), residues: 1992 helix: -0.87 (0.22), residues: 432 sheet: -3.45 (0.15), residues: 711 loop : -3.33 (0.16), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 52 HIS 0.002 0.001 HIS A 317 PHE 0.011 0.001 PHE K 91 TYR 0.015 0.001 TYR B 342 ARG 0.001 0.000 ARG A 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00673 ( 3) link_NAG-ASN : angle 2.46183 ( 9) hydrogen bonds : bond 0.21612 ( 657) hydrogen bonds : angle 8.67161 ( 1764) covalent geometry : bond 0.00369 (16035) covalent geometry : angle 0.60405 (21729) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 274 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8043 (mtpp) cc_final: 0.7515 (mtpp) REVERT: F 42 LYS cc_start: 0.8103 (mmtm) cc_final: 0.7771 (mtmt) REVERT: F 79 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6935 (mp10) REVERT: H 42 LYS cc_start: 0.8152 (mmtm) cc_final: 0.7768 (mtmt) REVERT: H 79 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.7207 (mp10) REVERT: B 274 MET cc_start: 0.8146 (mtp) cc_final: 0.7944 (mtt) REVERT: B 289 MET cc_start: 0.8512 (tpt) cc_final: 0.7838 (tpt) REVERT: K 37 GLN cc_start: 0.8382 (pt0) cc_final: 0.8119 (pt0) REVERT: K 79 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.7178 (mp10) REVERT: C 289 MET cc_start: 0.8488 (tpt) cc_final: 0.8070 (tpt) outliers start: 3 outliers final: 0 residues processed: 277 average time/residue: 0.3199 time to fit residues: 126.8966 Evaluate side-chains 178 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 175 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain K residue 79 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 7.9990 chunk 147 optimal weight: 0.0000 chunk 82 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 chunk 78 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN F 79 GLN A 254 ASN A 501 GLN H 79 GLN B 254 ASN B 501 GLN K 3 GLN K 79 GLN C 254 ASN C 501 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.136543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.109203 restraints weight = 22560.299| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.11 r_work: 0.3210 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 16038 Z= 0.195 Angle : 0.665 8.608 21738 Z= 0.344 Chirality : 0.048 0.269 2520 Planarity : 0.004 0.038 2736 Dihedral : 13.776 107.084 2214 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.67 % Allowed : 11.15 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -3.21 (0.17), residues: 1992 helix: 0.57 (0.24), residues: 432 sheet: -2.95 (0.15), residues: 684 loop : -2.76 (0.17), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 314 HIS 0.006 0.002 HIS B 317 PHE 0.022 0.002 PHE E 70 TYR 0.015 0.002 TYR C 299 ARG 0.002 0.000 ARG G 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00493 ( 3) link_NAG-ASN : angle 1.36139 ( 9) hydrogen bonds : bond 0.04403 ( 657) hydrogen bonds : angle 5.91373 ( 1764) covalent geometry : bond 0.00454 (16035) covalent geometry : angle 0.66457 (21729) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 1.727 Fit side-chains revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8278 (mtpp) cc_final: 0.7550 (mtpp) REVERT: D 82 GLN cc_start: 0.8411 (tt0) cc_final: 0.8129 (tt0) REVERT: F 42 LYS cc_start: 0.8203 (mmtm) cc_final: 0.7551 (mtmt) REVERT: F 73 LEU cc_start: 0.8611 (tt) cc_final: 0.8408 (tp) REVERT: A 95 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8583 (mm) REVERT: H 42 LYS cc_start: 0.8239 (mmtm) cc_final: 0.7541 (mtmt) REVERT: B 274 MET cc_start: 0.8427 (mtp) cc_final: 0.8139 (mtt) REVERT: G 82 GLN cc_start: 0.8356 (tt0) cc_final: 0.8100 (tt0) REVERT: C 289 MET cc_start: 0.8940 (tpt) cc_final: 0.8388 (tpt) outliers start: 30 outliers final: 19 residues processed: 211 average time/residue: 0.3094 time to fit residues: 95.0495 Evaluate side-chains 177 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 217 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 0 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 152 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 176 optimal weight: 0.4980 chunk 145 optimal weight: 0.0470 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN F 31 ASN H 3 GLN H 31 ASN K 3 GLN K 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.139650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.112496 restraints weight = 22121.215| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.09 r_work: 0.3256 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16038 Z= 0.131 Angle : 0.581 9.021 21738 Z= 0.299 Chirality : 0.044 0.309 2520 Planarity : 0.004 0.039 2736 Dihedral : 9.333 97.379 2205 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.29 % Allowed : 13.94 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.18), residues: 1992 helix: 1.29 (0.25), residues: 432 sheet: -2.45 (0.17), residues: 669 loop : -2.37 (0.18), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 314 HIS 0.004 0.001 HIS B 317 PHE 0.011 0.001 PHE G 70 TYR 0.023 0.002 TYR C 86 ARG 0.002 0.000 ARG B 507 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 3) link_NAG-ASN : angle 2.03562 ( 9) hydrogen bonds : bond 0.03677 ( 657) hydrogen bonds : angle 5.22326 ( 1764) covalent geometry : bond 0.00297 (16035) covalent geometry : angle 0.57987 (21729) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 3.649 Fit side-chains revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8168 (mtpp) cc_final: 0.7426 (mtpp) REVERT: D 81 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7857 (tp) REVERT: F 35 TRP cc_start: 0.7589 (m100) cc_final: 0.7353 (m100) REVERT: F 42 LYS cc_start: 0.8103 (mmtm) cc_final: 0.7458 (mtmt) REVERT: F 54 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8551 (tt) REVERT: A 95 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8529 (mm) REVERT: A 486 ASP cc_start: 0.7793 (p0) cc_final: 0.7374 (t0) REVERT: E 82 GLN cc_start: 0.8446 (tt0) cc_final: 0.8078 (tp40) REVERT: H 42 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7426 (mtmt) REVERT: H 54 LEU cc_start: 0.8705 (pp) cc_final: 0.8404 (tt) REVERT: B 274 MET cc_start: 0.8366 (mtp) cc_final: 0.8156 (mtt) REVERT: G 81 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7880 (tp) REVERT: K 54 LEU cc_start: 0.8816 (pp) cc_final: 0.8465 (tt) REVERT: C 289 MET cc_start: 0.9008 (tpt) cc_final: 0.8101 (tpt) outliers start: 41 outliers final: 27 residues processed: 229 average time/residue: 0.3432 time to fit residues: 117.0444 Evaluate side-chains 209 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 420 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 32 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 144 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN H 3 GLN K 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.135347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.106882 restraints weight = 22534.664| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.16 r_work: 0.3187 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16038 Z= 0.247 Angle : 0.665 9.670 21738 Z= 0.346 Chirality : 0.047 0.179 2520 Planarity : 0.004 0.039 2736 Dihedral : 8.087 83.898 2205 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.79 % Allowed : 15.33 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.18), residues: 1992 helix: 1.13 (0.25), residues: 432 sheet: -2.28 (0.17), residues: 669 loop : -2.34 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 314 HIS 0.007 0.002 HIS C 317 PHE 0.016 0.002 PHE F 91 TYR 0.022 0.002 TYR B 86 ARG 0.002 0.000 ARG D 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 3) link_NAG-ASN : angle 3.04571 ( 9) hydrogen bonds : bond 0.04460 ( 657) hydrogen bonds : angle 5.29852 ( 1764) covalent geometry : bond 0.00582 (16035) covalent geometry : angle 0.66241 (21729) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 181 time to evaluate : 1.663 Fit side-chains REVERT: D 13 LYS cc_start: 0.8248 (mtpp) cc_final: 0.8017 (mtpp) REVERT: D 48 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7684 (ptm) REVERT: F 42 LYS cc_start: 0.8108 (mmtm) cc_final: 0.7477 (mtmt) REVERT: F 45 GLN cc_start: 0.7591 (mt0) cc_final: 0.7389 (mm-40) REVERT: F 54 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8615 (tt) REVERT: A 95 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8499 (mm) REVERT: A 393 CYS cc_start: 0.7257 (m) cc_final: 0.6869 (m) REVERT: H 42 LYS cc_start: 0.8153 (mmtm) cc_final: 0.7407 (mtmt) REVERT: H 54 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8402 (tt) REVERT: B 274 MET cc_start: 0.8479 (mtp) cc_final: 0.8204 (mtt) REVERT: B 386 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8022 (tp) REVERT: G 82 GLN cc_start: 0.8406 (tt0) cc_final: 0.8119 (tp40) REVERT: K 54 LEU cc_start: 0.8839 (pp) cc_final: 0.8506 (tt) REVERT: C 289 MET cc_start: 0.9105 (tpt) cc_final: 0.8334 (tpt) outliers start: 50 outliers final: 30 residues processed: 211 average time/residue: 0.2845 time to fit residues: 88.7501 Evaluate side-chains 204 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 420 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 69 optimal weight: 0.0020 chunk 163 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 137 optimal weight: 0.4980 chunk 50 optimal weight: 0.7980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN H 3 GLN B 501 GLN K 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.139676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111598 restraints weight = 22563.051| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.19 r_work: 0.3260 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16038 Z= 0.114 Angle : 0.554 7.877 21738 Z= 0.288 Chirality : 0.042 0.172 2520 Planarity : 0.004 0.045 2736 Dihedral : 7.604 79.120 2205 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.68 % Allowed : 16.61 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.18), residues: 1992 helix: 1.72 (0.25), residues: 432 sheet: -1.93 (0.18), residues: 654 loop : -2.14 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 314 HIS 0.003 0.001 HIS B 317 PHE 0.010 0.001 PHE G 70 TYR 0.025 0.001 TYR C 86 ARG 0.002 0.000 ARG B 507 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 3) link_NAG-ASN : angle 3.14856 ( 9) hydrogen bonds : bond 0.03326 ( 657) hydrogen bonds : angle 4.84530 ( 1764) covalent geometry : bond 0.00264 (16035) covalent geometry : angle 0.55031 (21729) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 200 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8200 (mtpp) cc_final: 0.7972 (mtpp) REVERT: D 81 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7840 (tp) REVERT: F 42 LYS cc_start: 0.8119 (mmtm) cc_final: 0.7518 (mtmt) REVERT: A 95 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8486 (mm) REVERT: A 486 ASP cc_start: 0.7742 (p0) cc_final: 0.7136 (p0) REVERT: E 13 LYS cc_start: 0.8025 (mtpp) cc_final: 0.7800 (mtpp) REVERT: E 82 GLN cc_start: 0.8437 (tt0) cc_final: 0.8175 (tp40) REVERT: H 42 LYS cc_start: 0.8128 (mmtm) cc_final: 0.7449 (mtmt) REVERT: H 52 LYS cc_start: 0.8701 (mtmm) cc_final: 0.8107 (mttm) REVERT: H 54 LEU cc_start: 0.8689 (pp) cc_final: 0.8391 (tt) REVERT: K 52 LYS cc_start: 0.8846 (mttt) cc_final: 0.8545 (mtmm) REVERT: K 54 LEU cc_start: 0.8793 (pp) cc_final: 0.8469 (tt) REVERT: C 95 LEU cc_start: 0.8725 (mm) cc_final: 0.8411 (mm) REVERT: C 289 MET cc_start: 0.9127 (tpt) cc_final: 0.8208 (tpt) outliers start: 48 outliers final: 28 residues processed: 224 average time/residue: 0.2657 time to fit residues: 89.5052 Evaluate side-chains 211 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 405 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 88 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 127 optimal weight: 0.0670 overall best weight: 1.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN H 3 GLN K 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.135682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.107368 restraints weight = 22613.274| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.15 r_work: 0.3197 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16038 Z= 0.227 Angle : 0.645 9.729 21738 Z= 0.332 Chirality : 0.046 0.158 2520 Planarity : 0.004 0.038 2736 Dihedral : 7.750 76.883 2205 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.51 % Allowed : 16.72 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.18), residues: 1992 helix: 1.52 (0.25), residues: 432 sheet: -1.84 (0.18), residues: 642 loop : -2.20 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 314 HIS 0.007 0.002 HIS C 317 PHE 0.015 0.002 PHE F 91 TYR 0.028 0.002 TYR B 86 ARG 0.002 0.000 ARG D 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00097 ( 3) link_NAG-ASN : angle 3.39069 ( 9) hydrogen bonds : bond 0.04185 ( 657) hydrogen bonds : angle 5.01466 ( 1764) covalent geometry : bond 0.00532 (16035) covalent geometry : angle 0.64106 (21729) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 181 time to evaluate : 3.025 Fit side-chains REVERT: D 81 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7717 (tp) REVERT: F 42 LYS cc_start: 0.8073 (mmtm) cc_final: 0.7468 (mtmt) REVERT: A 95 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8517 (mm) REVERT: H 42 LYS cc_start: 0.8119 (mmtm) cc_final: 0.7455 (mtmt) REVERT: H 54 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8409 (tt) REVERT: B 386 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7753 (tp) REVERT: G 82 GLN cc_start: 0.8132 (tp40) cc_final: 0.7864 (mm110) REVERT: K 54 LEU cc_start: 0.8818 (pp) cc_final: 0.8480 (tt) REVERT: C 95 LEU cc_start: 0.8742 (mm) cc_final: 0.8378 (mm) REVERT: C 289 MET cc_start: 0.9163 (tpt) cc_final: 0.8236 (tpt) outliers start: 63 outliers final: 46 residues processed: 223 average time/residue: 0.4087 time to fit residues: 138.2953 Evaluate side-chains 221 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 171 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 467 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 191 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 145 optimal weight: 0.0570 chunk 84 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN H 3 GLN B 501 GLN K 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.138892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.111186 restraints weight = 22519.841| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.14 r_work: 0.3251 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16038 Z= 0.122 Angle : 0.560 8.080 21738 Z= 0.288 Chirality : 0.042 0.163 2520 Planarity : 0.003 0.044 2736 Dihedral : 7.425 74.823 2205 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.01 % Allowed : 17.95 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -1.52 (0.19), residues: 1992 helix: 1.85 (0.25), residues: 432 sheet: -1.61 (0.19), residues: 639 loop : -1.95 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 314 HIS 0.004 0.001 HIS A 317 PHE 0.010 0.001 PHE G 70 TYR 0.028 0.002 TYR B 86 ARG 0.001 0.000 ARG A 507 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 3) link_NAG-ASN : angle 3.33607 ( 9) hydrogen bonds : bond 0.03383 ( 657) hydrogen bonds : angle 4.72611 ( 1764) covalent geometry : bond 0.00285 (16035) covalent geometry : angle 0.55617 (21729) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 188 time to evaluate : 2.956 Fit side-chains revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8169 (mtpp) cc_final: 0.7522 (mtpp) REVERT: F 42 LYS cc_start: 0.8088 (mmtm) cc_final: 0.7491 (mtmt) REVERT: A 95 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8522 (mm) REVERT: A 251 MET cc_start: 0.9002 (mmp) cc_final: 0.8764 (mmp) REVERT: A 486 ASP cc_start: 0.7711 (p0) cc_final: 0.7071 (p0) REVERT: E 82 GLN cc_start: 0.8505 (tt0) cc_final: 0.8210 (tp40) REVERT: H 42 LYS cc_start: 0.8072 (mmtm) cc_final: 0.7425 (mtmt) REVERT: H 54 LEU cc_start: 0.8711 (pp) cc_final: 0.8415 (tt) REVERT: G 82 GLN cc_start: 0.8212 (tp40) cc_final: 0.7861 (mm110) REVERT: K 52 LYS cc_start: 0.8838 (mttt) cc_final: 0.8514 (mtmm) REVERT: K 54 LEU cc_start: 0.8776 (pp) cc_final: 0.8444 (tt) REVERT: C 95 LEU cc_start: 0.8740 (mm) cc_final: 0.8376 (mm) REVERT: C 289 MET cc_start: 0.9149 (tpt) cc_final: 0.8272 (tpt) outliers start: 54 outliers final: 38 residues processed: 217 average time/residue: 0.2815 time to fit residues: 91.6788 Evaluate side-chains 218 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 405 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 169 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 82 optimal weight: 0.2980 chunk 137 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN H 3 GLN B 225 GLN K 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.136601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.108261 restraints weight = 22357.653| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.17 r_work: 0.3210 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16038 Z= 0.195 Angle : 0.619 9.461 21738 Z= 0.317 Chirality : 0.045 0.170 2520 Planarity : 0.004 0.039 2736 Dihedral : 7.492 72.391 2205 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.34 % Allowed : 18.39 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.18), residues: 1992 helix: 1.68 (0.25), residues: 432 sheet: -1.59 (0.19), residues: 639 loop : -1.95 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 314 HIS 0.006 0.001 HIS C 317 PHE 0.013 0.002 PHE K 91 TYR 0.027 0.002 TYR B 86 ARG 0.002 0.000 ARG G 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00086 ( 3) link_NAG-ASN : angle 3.57205 ( 9) hydrogen bonds : bond 0.03910 ( 657) hydrogen bonds : angle 4.85809 ( 1764) covalent geometry : bond 0.00458 (16035) covalent geometry : angle 0.61491 (21729) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 177 time to evaluate : 1.810 Fit side-chains revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8222 (mtpp) cc_final: 0.7527 (mtpp) REVERT: F 42 LYS cc_start: 0.8083 (mmtm) cc_final: 0.7498 (mtmt) REVERT: A 95 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8549 (mm) REVERT: A 486 ASP cc_start: 0.7750 (p0) cc_final: 0.7123 (p0) REVERT: H 42 LYS cc_start: 0.8056 (mmtm) cc_final: 0.7429 (mtmt) REVERT: H 54 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8399 (tt) REVERT: G 82 GLN cc_start: 0.8238 (tp40) cc_final: 0.7883 (mm110) REVERT: K 52 LYS cc_start: 0.8863 (mttt) cc_final: 0.8549 (mtmm) REVERT: K 54 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8455 (tt) REVERT: C 95 LEU cc_start: 0.8747 (mm) cc_final: 0.8421 (mm) REVERT: C 289 MET cc_start: 0.9159 (tpt) cc_final: 0.8301 (tpt) outliers start: 60 outliers final: 47 residues processed: 210 average time/residue: 0.2854 time to fit residues: 89.1187 Evaluate side-chains 223 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 173 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 405 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 161 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 115 optimal weight: 0.0170 chunk 51 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN H 3 GLN B 225 GLN K 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.139720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111737 restraints weight = 22357.931| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.17 r_work: 0.3259 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16038 Z= 0.118 Angle : 0.562 7.727 21738 Z= 0.288 Chirality : 0.042 0.224 2520 Planarity : 0.003 0.043 2736 Dihedral : 7.169 70.359 2205 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.01 % Allowed : 19.01 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -1.26 (0.19), residues: 1992 helix: 1.98 (0.25), residues: 432 sheet: -1.46 (0.19), residues: 666 loop : -1.73 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 314 HIS 0.004 0.001 HIS B 317 PHE 0.009 0.001 PHE G 70 TYR 0.028 0.002 TYR B 86 ARG 0.001 0.000 ARG C 49 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 3) link_NAG-ASN : angle 3.54152 ( 9) hydrogen bonds : bond 0.03287 ( 657) hydrogen bonds : angle 4.64498 ( 1764) covalent geometry : bond 0.00277 (16035) covalent geometry : angle 0.55708 (21729) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 189 time to evaluate : 1.718 Fit side-chains revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8175 (mtpp) cc_final: 0.7479 (mtpp) REVERT: F 42 LYS cc_start: 0.8073 (mmtm) cc_final: 0.7466 (mtmt) REVERT: A 486 ASP cc_start: 0.7673 (p0) cc_final: 0.7003 (p0) REVERT: E 82 GLN cc_start: 0.8491 (tt0) cc_final: 0.8216 (tp40) REVERT: H 42 LYS cc_start: 0.8008 (mmtm) cc_final: 0.7363 (mtmt) REVERT: H 54 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8435 (tt) REVERT: G 82 GLN cc_start: 0.8251 (tp40) cc_final: 0.7909 (mm110) REVERT: K 52 LYS cc_start: 0.8814 (mttt) cc_final: 0.8492 (mtmm) REVERT: K 54 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8454 (tt) REVERT: C 95 LEU cc_start: 0.8722 (mm) cc_final: 0.8386 (mm) REVERT: C 289 MET cc_start: 0.9158 (tpt) cc_final: 0.8274 (tpt) outliers start: 54 outliers final: 43 residues processed: 217 average time/residue: 0.2705 time to fit residues: 87.7293 Evaluate side-chains 226 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 405 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 119 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN F 31 ASN A 225 GLN B 240 ASN K 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.134142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.105819 restraints weight = 22730.724| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.16 r_work: 0.3169 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 16038 Z= 0.310 Angle : 0.724 12.260 21738 Z= 0.371 Chirality : 0.049 0.228 2520 Planarity : 0.004 0.037 2736 Dihedral : 7.682 71.616 2205 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.62 % Allowed : 19.18 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -1.77 (0.18), residues: 1992 helix: 1.24 (0.24), residues: 432 sheet: -1.52 (0.20), residues: 630 loop : -2.09 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 314 HIS 0.009 0.002 HIS A 317 PHE 0.019 0.002 PHE F 91 TYR 0.037 0.003 TYR B 86 ARG 0.003 0.001 ARG C 336 Details of bonding type rmsd link_NAG-ASN : bond 0.00081 ( 3) link_NAG-ASN : angle 3.88534 ( 9) hydrogen bonds : bond 0.04700 ( 657) hydrogen bonds : angle 5.14918 ( 1764) covalent geometry : bond 0.00730 (16035) covalent geometry : angle 0.72021 (21729) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 1.714 Fit side-chains REVERT: D 13 LYS cc_start: 0.8257 (mtpp) cc_final: 0.7561 (mtpp) REVERT: D 82 GLN cc_start: 0.8376 (tp40) cc_final: 0.7936 (mm110) REVERT: F 42 LYS cc_start: 0.8127 (mmtm) cc_final: 0.7502 (mtmt) REVERT: A 486 ASP cc_start: 0.7801 (p0) cc_final: 0.7186 (p0) REVERT: H 42 LYS cc_start: 0.8081 (mmtm) cc_final: 0.7405 (mtmt) REVERT: G 82 GLN cc_start: 0.8312 (tp40) cc_final: 0.7937 (mm110) REVERT: K 52 LYS cc_start: 0.8861 (mttt) cc_final: 0.8571 (mtmm) REVERT: C 95 LEU cc_start: 0.8724 (mm) cc_final: 0.8439 (mm) REVERT: C 289 MET cc_start: 0.9207 (tpt) cc_final: 0.8328 (tpt) outliers start: 47 outliers final: 42 residues processed: 203 average time/residue: 0.2883 time to fit residues: 87.1486 Evaluate side-chains 211 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 405 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 68 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 190 optimal weight: 0.9980 chunk 166 optimal weight: 0.0570 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN F 31 ASN K 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.138838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.110676 restraints weight = 22385.999| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.17 r_work: 0.3245 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16038 Z= 0.122 Angle : 0.584 8.822 21738 Z= 0.298 Chirality : 0.043 0.216 2520 Planarity : 0.003 0.043 2736 Dihedral : 7.223 69.490 2205 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.62 % Allowed : 19.23 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -1.35 (0.19), residues: 1992 helix: 1.76 (0.25), residues: 432 sheet: -1.47 (0.19), residues: 669 loop : -1.73 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 314 HIS 0.003 0.001 HIS A 317 PHE 0.007 0.001 PHE K 91 TYR 0.027 0.002 TYR B 86 ARG 0.001 0.000 ARG A 507 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 3) link_NAG-ASN : angle 3.62718 ( 9) hydrogen bonds : bond 0.03418 ( 657) hydrogen bonds : angle 4.75250 ( 1764) covalent geometry : bond 0.00288 (16035) covalent geometry : angle 0.57957 (21729) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9995.70 seconds wall clock time: 177 minutes 45.34 seconds (10665.34 seconds total)