Starting phenix.real_space_refine on Mon Jan 20 19:44:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wz3_37945/01_2025/8wz3_37945.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wz3_37945/01_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_37945/01_2025/8wz3_37945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wz3_37945/01_2025/8wz3_37945.map" model { file = "/net/cci-nas-00/data/ceres_data/8wz3_37945/01_2025/8wz3_37945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wz3_37945/01_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-5571/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: 9.96, per 1000 atoms: 0.63 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: 4.50 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: 2.65 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: 7.70 Time building geometry restraints manager: 4.19 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: 0.11 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: 2.660 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: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 39.380 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.430 ------------------------------------------------------------------------------- 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 16035 Z= 0.232 Angle : 0.604 6.942 21729 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 *********************** 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 : 1.901 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: 0.3084 time to fit residues: 122.1429 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 : 1.803 ------------------------------------------------------------------------------- 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 = 0.136538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.109188 restraints weight = 22561.184| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.11 r_work: 0.3212 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 16035 Z= 0.294 Angle : 0.665 8.616 21729 Z= 0.344 Chirality : 0.048 0.270 2520 Planarity : 0.004 0.038 2736 Dihedral : 13.767 107.090 2214 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.67 % Allowed : 11.09 % Favored : 87.24 % 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 *********************** 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 : 1.678 Fit side-chains revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8268 (mtpp) cc_final: 0.7537 (mtpp) REVERT: D 82 GLN cc_start: 0.8409 (tt0) cc_final: 0.8124 (tt0) REVERT: F 42 LYS cc_start: 0.8175 (mmtm) cc_final: 0.7514 (mtmt) REVERT: A 95 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8564 (mm) REVERT: H 42 LYS cc_start: 0.8213 (mmtm) cc_final: 0.7507 (mtmt) REVERT: B 274 MET cc_start: 0.8415 (mtp) cc_final: 0.8123 (mtt) REVERT: G 82 GLN cc_start: 0.8352 (tt0) cc_final: 0.8093 (tt0) REVERT: C 289 MET cc_start: 0.8939 (tpt) cc_final: 0.8387 (tpt) outliers start: 30 outliers final: 19 residues processed: 211 average time/residue: 0.3055 time to fit residues: 94.8899 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 : 1.630 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 181 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 176 optimal weight: 0.7980 chunk 145 optimal weight: 0.3980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.138689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.110467 restraints weight = 22241.491| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.16 r_work: 0.3248 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16035 Z= 0.207 Angle : 0.584 8.970 21729 Z= 0.302 Chirality : 0.044 0.302 2520 Planarity : 0.004 0.038 2736 Dihedral : 9.180 95.970 2205 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.29 % Allowed : 13.88 % Favored : 83.84 % 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: -2.45 (0.17), residues: 1992 helix: 1.24 (0.25), residues: 432 sheet: -2.42 (0.17), residues: 666 loop : -2.39 (0.18), residues: 894 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 E 70 TYR 0.021 0.002 TYR C 86 ARG 0.001 0.000 ARG H 24 *********************** 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 251 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 2.001 Fit side-chains revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8162 (mtpp) cc_final: 0.7409 (mtpp) REVERT: F 42 LYS cc_start: 0.8073 (mmtm) cc_final: 0.7420 (mtmt) REVERT: F 54 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8539 (tt) REVERT: A 95 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8504 (mm) REVERT: A 486 ASP cc_start: 0.7816 (p0) cc_final: 0.7381 (t0) REVERT: E 82 GLN cc_start: 0.8465 (tt0) cc_final: 0.8094 (tp40) REVERT: H 42 LYS cc_start: 0.8096 (mmtm) cc_final: 0.7382 (mtmt) REVERT: H 54 LEU cc_start: 0.8689 (pp) cc_final: 0.8384 (tt) REVERT: B 274 MET cc_start: 0.8367 (mtp) cc_final: 0.8159 (mtt) REVERT: K 54 LEU cc_start: 0.8811 (pp) cc_final: 0.8469 (tt) REVERT: C 289 MET cc_start: 0.9012 (tpt) cc_final: 0.8102 (tpt) outliers start: 41 outliers final: 30 residues processed: 230 average time/residue: 0.3267 time to fit residues: 114.0673 Evaluate side-chains 208 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 1.898 ------------------------------------------------------------------------------- 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 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 217 ILE 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 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 292 ILE 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: 0.8980 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.135690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.107345 restraints weight = 22504.903| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.16 r_work: 0.3193 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16035 Z= 0.357 Angle : 0.645 9.385 21729 Z= 0.337 Chirality : 0.046 0.173 2520 Planarity : 0.004 0.038 2736 Dihedral : 8.014 83.206 2205 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.01 % Allowed : 15.11 % 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: -2.33 (0.18), residues: 1992 helix: 1.20 (0.25), residues: 432 sheet: -2.25 (0.17), residues: 669 loop : -2.33 (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 0.015 0.002 PHE F 91 TYR 0.030 0.002 TYR C 86 ARG 0.002 0.000 ARG D 98 *********************** 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 238 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 184 time to evaluate : 1.853 Fit side-chains revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8246 (mtpp) cc_final: 0.8013 (mtpp) REVERT: D 81 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7717 (tp) REVERT: D 82 GLN cc_start: 0.8449 (tt0) cc_final: 0.8246 (tp40) REVERT: F 42 LYS cc_start: 0.8104 (mmtm) cc_final: 0.7473 (mtmt) REVERT: F 45 GLN cc_start: 0.7583 (mt0) cc_final: 0.7375 (mm-40) REVERT: F 54 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8608 (tt) REVERT: A 95 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8525 (mm) REVERT: A 393 CYS cc_start: 0.7167 (m) cc_final: 0.6802 (m) REVERT: H 42 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7393 (mtmt) REVERT: H 54 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8352 (tt) REVERT: B 274 MET cc_start: 0.8475 (mtp) cc_final: 0.8214 (mtt) REVERT: G 82 GLN cc_start: 0.8394 (tt0) cc_final: 0.8114 (tp40) REVERT: C 200 ASP cc_start: 0.6805 (m-30) cc_final: 0.6599 (m-30) REVERT: C 289 MET cc_start: 0.9102 (tpt) cc_final: 0.8273 (tpt) REVERT: C 393 CYS cc_start: 0.7089 (m) cc_final: 0.6569 (m) outliers start: 54 outliers final: 38 residues processed: 214 average time/residue: 0.3067 time to fit residues: 97.8366 Evaluate side-chains 215 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 1.803 ------------------------------------------------------------------------------- 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 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 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 217 ILE 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 217 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 382 CYS 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 18 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 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 382 CYS 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: 0.5980 chunk 163 optimal weight: 0.8980 chunk 169 optimal weight: 0.0270 chunk 136 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 137 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.140233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.112227 restraints weight = 22575.171| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.19 r_work: 0.3268 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16035 Z= 0.162 Angle : 0.539 7.889 21729 Z= 0.282 Chirality : 0.042 0.173 2520 Planarity : 0.004 0.047 2736 Dihedral : 7.521 78.328 2205 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.29 % Allowed : 17.06 % Favored : 80.66 % 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: -1.80 (0.18), residues: 1992 helix: 1.83 (0.25), residues: 432 sheet: -1.91 (0.18), residues: 654 loop : -2.13 (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 0.009 0.001 PHE G 70 TYR 0.021 0.001 TYR B 86 ARG 0.001 0.000 ARG B 507 *********************** 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 244 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 203 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8155 (mtpp) cc_final: 0.7921 (mtpp) REVERT: D 81 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7852 (tp) REVERT: F 42 LYS cc_start: 0.8113 (mmtm) cc_final: 0.7506 (mtmt) REVERT: F 54 LEU cc_start: 0.8825 (pp) cc_final: 0.8607 (tt) REVERT: A 95 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8488 (mm) REVERT: A 486 ASP cc_start: 0.7730 (p0) cc_final: 0.7134 (p0) REVERT: E 13 LYS cc_start: 0.8031 (mtpp) cc_final: 0.7814 (mtpp) REVERT: E 82 GLN cc_start: 0.8443 (tt0) cc_final: 0.8186 (tp40) REVERT: H 42 LYS cc_start: 0.8117 (mmtm) cc_final: 0.7439 (mtmt) REVERT: H 52 LYS cc_start: 0.8715 (mtmm) cc_final: 0.8106 (mttm) REVERT: H 54 LEU cc_start: 0.8681 (pp) cc_final: 0.8387 (tt) REVERT: B 386 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7728 (tp) REVERT: K 52 LYS cc_start: 0.8820 (mttt) cc_final: 0.8516 (mtmm) REVERT: K 54 LEU cc_start: 0.8772 (pp) cc_final: 0.8482 (tt) REVERT: C 95 LEU cc_start: 0.8704 (mm) cc_final: 0.8363 (mm) REVERT: C 251 MET cc_start: 0.8849 (mmp) cc_final: 0.8604 (mmp) REVERT: C 289 MET cc_start: 0.9126 (tpt) cc_final: 0.8183 (tpt) outliers start: 41 outliers final: 24 residues processed: 222 average time/residue: 0.2731 time to fit residues: 91.1892 Evaluate side-chains 212 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 1.884 ------------------------------------------------------------------------------- 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 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 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 217 ILE Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 386 ILE 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 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: 2.9990 chunk 4 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 127 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 H 3 GLN B 240 ASN K 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.133890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105487 restraints weight = 22675.060| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.16 r_work: 0.3168 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 16035 Z= 0.478 Angle : 0.708 11.153 21729 Z= 0.367 Chirality : 0.048 0.210 2520 Planarity : 0.004 0.038 2736 Dihedral : 7.933 76.657 2205 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.01 % Allowed : 16.50 % Favored : 79.49 % 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: -2.14 (0.18), residues: 1992 helix: 1.24 (0.25), residues: 432 sheet: -1.99 (0.18), residues: 657 loop : -2.27 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 314 HIS 0.010 0.002 HIS B 317 PHE 0.019 0.002 PHE F 91 TYR 0.031 0.003 TYR B 86 ARG 0.003 0.001 ARG D 98 *********************** 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 240 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 168 time to evaluate : 2.199 Fit side-chains REVERT: D 81 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7592 (tp) REVERT: F 42 LYS cc_start: 0.8089 (mmtm) cc_final: 0.7463 (mtmt) REVERT: F 54 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8605 (tt) REVERT: A 95 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8520 (mm) REVERT: H 42 LYS cc_start: 0.8148 (mmtm) cc_final: 0.7468 (mtmt) REVERT: C 95 LEU cc_start: 0.8770 (mm) cc_final: 0.8421 (mm) REVERT: C 289 MET cc_start: 0.9140 (tpt) cc_final: 0.8314 (tpt) outliers start: 72 outliers final: 53 residues processed: 215 average time/residue: 0.2933 time to fit residues: 93.9593 Evaluate side-chains 217 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 161 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 18 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 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 58 VAL 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 292 ILE Chi-restraints excluded: chain A residue 382 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 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 69 THR Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 73 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 382 CYS Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain G residue 18 VAL 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 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 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 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: 3.9990 chunk 50 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 145 optimal weight: 0.0470 chunk 84 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 164 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 B 501 GLN K 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.138063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.110171 restraints weight = 22560.707| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.16 r_work: 0.3244 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 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 : 0.003 0.050 16035 Z= 0.180 Angle : 0.562 8.787 21729 Z= 0.291 Chirality : 0.043 0.162 2520 Planarity : 0.004 0.044 2736 Dihedral : 7.544 75.273 2205 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.79 % Allowed : 18.67 % Favored : 78.54 % 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: -1.66 (0.18), residues: 1992 helix: 1.74 (0.25), residues: 432 sheet: -1.69 (0.19), residues: 639 loop : -2.05 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 314 HIS 0.004 0.001 HIS A 317 PHE 0.010 0.001 PHE G 70 TYR 0.031 0.002 TYR B 86 ARG 0.001 0.000 ARG A 507 *********************** 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 235 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 185 time to evaluate : 1.948 Fit side-chains revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8164 (mtpp) cc_final: 0.7474 (mtpp) REVERT: F 42 LYS cc_start: 0.8055 (mmtm) cc_final: 0.7443 (mtmt) REVERT: F 54 LEU cc_start: 0.8806 (pp) cc_final: 0.8589 (tt) REVERT: A 95 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8532 (mm) REVERT: A 251 MET cc_start: 0.8986 (mmp) cc_final: 0.8745 (mmp) REVERT: A 486 ASP cc_start: 0.7759 (p0) cc_final: 0.7133 (p0) REVERT: E 81 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7770 (tp) REVERT: E 82 GLN cc_start: 0.8512 (tt0) cc_final: 0.8217 (tp40) REVERT: H 42 LYS cc_start: 0.8095 (mmtm) cc_final: 0.7433 (mtmt) REVERT: H 54 LEU cc_start: 0.8676 (pp) cc_final: 0.8367 (tt) REVERT: B 158 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8446 (mp) REVERT: K 52 LYS cc_start: 0.8831 (mttt) cc_final: 0.8507 (mtmm) REVERT: K 54 LEU cc_start: 0.8780 (pp) cc_final: 0.8458 (tt) REVERT: C 95 LEU cc_start: 0.8721 (mm) cc_final: 0.8381 (mm) REVERT: C 289 MET cc_start: 0.9149 (tpt) cc_final: 0.8319 (tpt) outliers start: 50 outliers final: 34 residues processed: 213 average time/residue: 0.2856 time to fit residues: 91.3500 Evaluate side-chains 212 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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 78 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 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 E residue 81 LEU 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 158 LEU 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 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 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 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: 2.9990 chunk 155 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN A 225 GLN H 3 GLN B 225 GLN K 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.136666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.108267 restraints weight = 22370.902| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.17 r_work: 0.3215 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16035 Z= 0.284 Angle : 0.611 9.615 21729 Z= 0.315 Chirality : 0.044 0.154 2520 Planarity : 0.004 0.039 2736 Dihedral : 7.553 72.704 2205 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.90 % Allowed : 18.78 % Favored : 78.32 % 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: -1.68 (0.18), residues: 1992 helix: 1.64 (0.25), residues: 432 sheet: -1.66 (0.19), residues: 636 loop : -2.06 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 314 HIS 0.006 0.001 HIS A 317 PHE 0.013 0.001 PHE K 91 TYR 0.030 0.002 TYR B 86 ARG 0.001 0.000 ARG E 98 *********************** 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 228 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 1.871 Fit side-chains revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8225 (mtpp) cc_final: 0.7510 (mtpp) REVERT: F 42 LYS cc_start: 0.8087 (mmtm) cc_final: 0.7491 (mtmt) REVERT: F 54 LEU cc_start: 0.8827 (pp) cc_final: 0.8589 (tt) REVERT: A 95 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8534 (mm) REVERT: A 486 ASP cc_start: 0.7768 (p0) cc_final: 0.7134 (p0) REVERT: H 42 LYS cc_start: 0.8079 (mmtm) cc_final: 0.7435 (mtmt) REVERT: K 54 LEU cc_start: 0.8798 (pp) cc_final: 0.8461 (tt) REVERT: C 95 LEU cc_start: 0.8734 (mm) cc_final: 0.8420 (mm) REVERT: C 289 MET cc_start: 0.9172 (tpt) cc_final: 0.8311 (tpt) outliers start: 52 outliers final: 44 residues processed: 207 average time/residue: 0.2920 time to fit residues: 90.8374 Evaluate side-chains 217 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 1.672 ------------------------------------------------------------------------------- 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 58 VAL Chi-restraints excluded: chain F residue 72 SER 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 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 72 SER Chi-restraints excluded: chain H residue 73 LEU 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 G residue 18 VAL 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 G residue 113 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 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 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: 0.6980 chunk 98 optimal weight: 0.9980 chunk 187 optimal weight: 0.1980 chunk 84 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 115 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.139914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.111874 restraints weight = 22295.589| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.17 r_work: 0.3265 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16035 Z= 0.167 Angle : 0.548 7.558 21729 Z= 0.283 Chirality : 0.043 0.223 2520 Planarity : 0.003 0.044 2736 Dihedral : 7.196 70.461 2205 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.56 % Allowed : 19.23 % 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: -1.32 (0.19), residues: 1992 helix: 1.99 (0.25), residues: 432 sheet: -1.50 (0.19), residues: 666 loop : -1.78 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 314 HIS 0.003 0.001 HIS B 317 PHE 0.010 0.001 PHE D 70 TYR 0.025 0.001 TYR B 86 ARG 0.001 0.000 ARG A 507 *********************** 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 237 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 191 time to evaluate : 2.109 Fit side-chains revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7489 (mtpp) REVERT: F 42 LYS cc_start: 0.8090 (mmtm) cc_final: 0.7508 (mtmt) REVERT: F 52 LYS cc_start: 0.8786 (mttt) cc_final: 0.8316 (mmtt) REVERT: A 251 MET cc_start: 0.8968 (mmp) cc_final: 0.8735 (mmp) REVERT: A 486 ASP cc_start: 0.7684 (p0) cc_final: 0.7105 (p0) REVERT: E 82 GLN cc_start: 0.8466 (tt0) cc_final: 0.8197 (tp40) REVERT: H 42 LYS cc_start: 0.8064 (mmtm) cc_final: 0.7464 (mtmt) REVERT: H 54 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8423 (tt) REVERT: K 52 LYS cc_start: 0.8831 (mttt) cc_final: 0.8522 (mtmm) REVERT: K 54 LEU cc_start: 0.8756 (pp) cc_final: 0.8439 (tt) REVERT: C 95 LEU cc_start: 0.8703 (mm) cc_final: 0.8356 (mm) REVERT: C 251 MET cc_start: 0.8836 (mmp) cc_final: 0.8500 (mmp) REVERT: C 289 MET cc_start: 0.9162 (tpt) cc_final: 0.8271 (tpt) outliers start: 46 outliers final: 35 residues processed: 215 average time/residue: 0.2980 time to fit residues: 95.9443 Evaluate side-chains 216 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 1.869 ------------------------------------------------------------------------------- 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 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 72 SER 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 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 72 SER Chi-restraints excluded: chain H residue 73 LEU 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 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 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 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: 0.8980 chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN B 225 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 = 0.3686 r_free = 0.3686 target = 0.135278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.106825 restraints weight = 22669.201| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.18 r_work: 0.3190 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16035 Z= 0.383 Angle : 0.666 10.773 21729 Z= 0.343 Chirality : 0.047 0.238 2520 Planarity : 0.004 0.038 2736 Dihedral : 7.497 70.927 2205 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.68 % Allowed : 18.90 % Favored : 78.43 % 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: -1.64 (0.18), residues: 1992 helix: 1.47 (0.25), residues: 432 sheet: -1.53 (0.19), residues: 636 loop : -2.00 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 314 HIS 0.009 0.002 HIS A 317 PHE 0.016 0.002 PHE F 91 TYR 0.029 0.002 TYR B 86 ARG 0.002 0.000 ARG A 364 ********************** 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 222 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 2.025 Fit side-chains REVERT: D 13 LYS cc_start: 0.8250 (mtpp) cc_final: 0.7557 (mtpp) REVERT: F 42 LYS cc_start: 0.8124 (mmtm) cc_final: 0.7527 (mtmt) REVERT: A 486 ASP cc_start: 0.7752 (p0) cc_final: 0.7122 (p0) REVERT: H 42 LYS cc_start: 0.8057 (mmtm) cc_final: 0.7415 (mtmt) REVERT: K 52 LYS cc_start: 0.8868 (mttt) cc_final: 0.8561 (mtmm) REVERT: K 54 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8474 (tt) REVERT: C 95 LEU cc_start: 0.8750 (mm) cc_final: 0.8446 (mm) REVERT: C 289 MET cc_start: 0.9202 (tpt) cc_final: 0.8304 (tpt) outliers start: 48 outliers final: 43 residues processed: 205 average time/residue: 0.2888 time to fit residues: 88.4960 Evaluate side-chains 215 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 1.810 ------------------------------------------------------------------------------- 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 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 F residue 54 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 72 SER 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 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 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 72 SER Chi-restraints excluded: chain H residue 73 LEU 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 G residue 37 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 113 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 393 CYS Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 467 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 68 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 194 optimal weight: 0.9980 chunk 38 optimal weight: 0.0670 chunk 190 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN K 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.138240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.109993 restraints weight = 22335.214| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.17 r_work: 0.3233 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 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 0.068 16035 Z= 0.217 Angle : 0.585 9.231 21729 Z= 0.300 Chirality : 0.044 0.245 2520 Planarity : 0.003 0.041 2736 Dihedral : 7.241 69.477 2205 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.56 % Allowed : 18.84 % Favored : 78.60 % 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: -1.39 (0.19), residues: 1992 helix: 1.72 (0.25), residues: 432 sheet: -1.48 (0.19), residues: 669 loop : -1.77 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 314 HIS 0.004 0.001 HIS A 317 PHE 0.009 0.001 PHE F 91 TYR 0.026 0.002 TYR B 86 ARG 0.001 0.000 ARG A 507 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8294.60 seconds wall clock time: 151 minutes 53.33 seconds (9113.33 seconds total)