Starting phenix.real_space_refine on Tue Dec 31 12:37:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wz3_37945/12_2024/8wz3_37945.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wz3_37945/12_2024/8wz3_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_37945/12_2024/8wz3_37945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wz3_37945/12_2024/8wz3_37945.map" model { file = "/net/cci-nas-00/data/ceres_data/8wz3_37945/12_2024/8wz3_37945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wz3_37945/12_2024/8wz3_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-5532/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: 9.80, per 1000 atoms: 0.62 Number of scatterers: 15741 At special positions: 0 Unit cell: (138.484, 150.154, 123.702, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3087 8.00 N 2577 7.00 C 9987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 500 " " NAG B 601 " - " ASN B 500 " " NAG C 601 " - " ASN C 500 " Time building additional restraints: 3.41 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: 2.46 Creating SS restraints... Processing helix chain 'D' and resid 62 through 65 removed outlier: 4.184A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.954A pdb=" N THR D 91 " --> pdb=" O ASN D 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 98 Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.859A pdb=" N LEU A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 142 " --> pdb=" O GLY A 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 138 through 142' Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 195 through 209 Proline residue: A 205 - end of helix Processing helix chain 'A' and resid 217 through 241 removed outlier: 3.805A pdb=" N ILE A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 262 Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 277 through 283 Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.750A pdb=" N SER A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 385 Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 491 through 512 Processing helix chain 'E' and resid 62 through 65 removed outlier: 4.184A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.955A pdb=" N THR E 91 " --> pdb=" O ASN E 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 98 Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.859A pdb=" N LEU B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU B 142 " --> pdb=" O GLY B 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 138 through 142' Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 195 through 209 Proline residue: B 205 - end of helix Processing helix chain 'B' and resid 217 through 241 removed outlier: 3.805A pdb=" N ILE B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 262 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.750A pdb=" N SER B 372 " --> pdb=" O THR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 385 Processing helix chain 'B' and resid 473 through 477 Processing helix chain 'B' and resid 491 through 512 Processing helix chain 'G' and resid 62 through 65 removed outlier: 4.184A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.955A pdb=" N THR G 91 " --> pdb=" O ASN G 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 98 Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.859A pdb=" N LEU C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU C 142 " --> pdb=" O GLY C 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 138 through 142' Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 195 through 209 Proline residue: C 205 - end of helix Processing helix chain 'C' and resid 217 through 241 removed outlier: 3.805A pdb=" N ILE C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 262 Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 277 through 283 Processing helix chain 'C' and resid 368 through 372 removed outlier: 3.750A pdb=" N SER C 372 " --> pdb=" O THR C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 385 Processing helix chain 'C' and resid 473 through 477 Processing helix chain 'C' and resid 491 through 512 Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.509A pdb=" N VAL D 18 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.634A pdb=" N THR D 113 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR D 110 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR D 94 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 93 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.634A pdb=" N THR D 113 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR D 110 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR D 94 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG D 98 " --> pdb=" O TYR D 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.794A pdb=" N GLN F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 12 through 13 Processing sheet with id=AA6, first strand: chain 'F' and resid 45 through 46 Processing sheet with id=AA7, first strand: chain 'A' and resid 373 through 375 removed outlier: 3.663A pdb=" N TRP A 341 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU A 30 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL A 469 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE A 32 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 179 through 180 removed outlier: 10.336A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 192 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA A 47 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE A 309 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N ARG A 49 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY A 307 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 301 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA A 298 " --> pdb=" O CYS A 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 179 through 180 removed outlier: 10.336A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 192 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 333 through 336 removed outlier: 3.894A pdb=" N SER A 398 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 404 through 407 removed outlier: 3.536A pdb=" N CYS A 416 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 431 through 434 Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.509A pdb=" N VAL E 18 " --> pdb=" O ILE E 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.633A pdb=" N THR E 113 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR E 110 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR E 94 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E 93 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.633A pdb=" N THR E 113 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR E 110 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR E 94 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG E 98 " --> pdb=" O TYR E 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.793A pdb=" N GLN H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 12 through 13 Processing sheet with id=AB9, first strand: chain 'H' and resid 45 through 46 Processing sheet with id=AC1, first strand: chain 'B' and resid 373 through 375 removed outlier: 3.663A pdb=" N TRP B 341 " --> pdb=" O PHE B 352 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU B 30 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL B 469 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE B 32 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 179 through 180 removed outlier: 10.336A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 192 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA B 47 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE B 309 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N ARG B 49 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY B 307 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 301 " --> pdb=" O SER B 55 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA B 298 " --> pdb=" O CYS B 290 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 179 through 180 removed outlier: 10.336A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 192 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 333 through 336 removed outlier: 3.895A pdb=" N SER B 398 " --> pdb=" O CYS B 333 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 404 through 407 removed outlier: 3.536A pdb=" N CYS B 416 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 431 through 434 Processing sheet with id=AC7, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.509A pdb=" N VAL G 18 " --> pdb=" O ILE G 83 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.633A pdb=" N THR G 113 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR G 110 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR G 94 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE G 93 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.633A pdb=" N THR G 113 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR G 110 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR G 94 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG G 98 " --> pdb=" O TYR G 105 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.794A pdb=" N GLN K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 12 through 13 Processing sheet with id=AD3, first strand: chain 'K' and resid 45 through 46 Processing sheet with id=AD4, first strand: chain 'C' and resid 373 through 375 removed outlier: 3.662A pdb=" N TRP C 341 " --> pdb=" O PHE C 352 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU C 30 " --> pdb=" O LEU C 467 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL C 469 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE C 32 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 179 through 180 removed outlier: 10.336A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 192 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA C 47 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE C 309 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N ARG C 49 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY C 307 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL C 301 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA C 298 " --> pdb=" O CYS C 290 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 179 through 180 removed outlier: 10.336A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 192 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 333 through 336 removed outlier: 3.894A pdb=" N SER C 398 " --> pdb=" O CYS C 333 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 404 through 407 removed outlier: 3.536A pdb=" N CYS C 416 " --> pdb=" O GLY C 438 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 431 through 434 684 hydrogen bonds defined for protein. 1764 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.72 Time building geometry restraints manager: 4.03 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' 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: 4.260 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: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 37.310 Find NCS groups from input model: 0.570 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: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.960 ------------------------------------------------------------------------------- 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 : 1.423 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: 0.3147 time to fit residues: 125.2009 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 : 1.943 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 : 1.837 Fit side-chains revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8058 (mtpp) cc_final: 0.7525 (mtpp) REVERT: D 82 GLN cc_start: 0.7608 (tt0) cc_final: 0.7402 (tt0) REVERT: F 42 LYS cc_start: 0.8186 (mmtm) cc_final: 0.7930 (mtmt) REVERT: F 73 LEU cc_start: 0.8685 (tt) cc_final: 0.8461 (tp) REVERT: H 42 LYS cc_start: 0.8248 (mmtm) cc_final: 0.7940 (mtmt) REVERT: B 274 MET cc_start: 0.8112 (mtp) cc_final: 0.7881 (mtt) REVERT: C 289 MET cc_start: 0.8746 (tpt) cc_final: 0.8210 (tpt) outliers start: 30 outliers final: 19 residues processed: 211 average time/residue: 0.3098 time to fit residues: 95.7695 Evaluate side-chains 175 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 2.600 ------------------------------------------------------------------------------- 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 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 98 optimal weight: 0.0870 chunk 54 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16035 Z= 0.391 Angle : 0.701 10.278 21729 Z= 0.360 Chirality : 0.048 0.313 2520 Planarity : 0.004 0.039 2736 Dihedral : 9.916 99.523 2205 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.40 % Allowed : 15.33 % Favored : 82.27 % 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: -2.82 (0.17), residues: 1992 helix: 0.72 (0.24), residues: 432 sheet: -2.60 (0.16), residues: 672 loop : -2.53 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 314 HIS 0.007 0.002 HIS C 317 PHE 0.015 0.002 PHE F 91 TYR 0.023 0.002 TYR C 86 ARG 0.002 0.000 ARG G 67 *********************** 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 214 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 1.783 Fit side-chains REVERT: D 13 LYS cc_start: 0.8064 (mtpp) cc_final: 0.7505 (mtpp) REVERT: D 48 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7577 (ptm) REVERT: B 274 MET cc_start: 0.8134 (mtp) cc_final: 0.7933 (mtt) REVERT: C 289 MET cc_start: 0.8831 (tpt) cc_final: 0.8095 (tpt) outliers start: 43 outliers final: 32 residues processed: 196 average time/residue: 0.3098 time to fit residues: 89.3527 Evaluate side-chains 191 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 1.771 ------------------------------------------------------------------------------- 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 11 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 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 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 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 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 175 optimal weight: 0.4980 chunk 133 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 H 31 ASN B 501 GLN K 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16035 Z= 0.213 Angle : 0.585 8.981 21729 Z= 0.304 Chirality : 0.043 0.186 2520 Planarity : 0.004 0.039 2736 Dihedral : 8.028 86.468 2205 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.45 % Allowed : 16.22 % Favored : 81.33 % 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: -2.29 (0.18), residues: 1992 helix: 1.23 (0.24), residues: 432 sheet: -2.26 (0.17), residues: 666 loop : -2.27 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 314 HIS 0.005 0.001 HIS A 317 PHE 0.010 0.001 PHE E 70 TYR 0.029 0.002 TYR C 86 ARG 0.002 0.000 ARG B 507 *********************** 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 246 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 202 time to evaluate : 1.848 Fit side-chains REVERT: D 13 LYS cc_start: 0.8023 (mtpp) cc_final: 0.7454 (mtpp) REVERT: D 81 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7691 (tp) REVERT: F 42 LYS cc_start: 0.8323 (mptt) cc_final: 0.7854 (mtmt) REVERT: A 486 ASP cc_start: 0.7117 (p0) cc_final: 0.6544 (p0) REVERT: C 289 MET cc_start: 0.8888 (tpt) cc_final: 0.8042 (tpt) outliers start: 44 outliers final: 35 residues processed: 222 average time/residue: 0.3085 time to fit residues: 102.1698 Evaluate side-chains 214 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain 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 58 THR Chi-restraints excluded: chain A residue 217 ILE 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 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 73 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 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 420 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16035 Z= 0.335 Angle : 0.639 10.158 21729 Z= 0.330 Chirality : 0.045 0.169 2520 Planarity : 0.004 0.038 2736 Dihedral : 7.955 82.212 2205 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.90 % Allowed : 16.89 % Favored : 79.21 % 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: -2.17 (0.18), residues: 1992 helix: 1.29 (0.24), residues: 432 sheet: -2.12 (0.18), residues: 666 loop : -2.23 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 314 HIS 0.007 0.002 HIS A 317 PHE 0.014 0.001 PHE K 91 TYR 0.024 0.002 TYR B 86 ARG 0.002 0.000 ARG G 67 *********************** 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 251 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 181 time to evaluate : 1.902 Fit side-chains REVERT: D 81 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7554 (tp) REVERT: A 393 CYS cc_start: 0.5246 (m) cc_final: 0.4908 (m) REVERT: C 289 MET cc_start: 0.8927 (tpt) cc_final: 0.8066 (tpt) REVERT: C 393 CYS cc_start: 0.5122 (m) cc_final: 0.4667 (m) outliers start: 70 outliers final: 51 residues processed: 225 average time/residue: 0.3107 time to fit residues: 103.4177 Evaluate side-chains 217 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 165 time to evaluate : 1.840 ------------------------------------------------------------------------------- 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 4 MET 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 A residue 58 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 220 VAL 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 73 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 422 CYS 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 20 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 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 405 SER Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 422 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16035 Z= 0.259 Angle : 0.602 9.490 21729 Z= 0.311 Chirality : 0.044 0.165 2520 Planarity : 0.004 0.040 2736 Dihedral : 7.810 80.149 2205 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.40 % Allowed : 17.84 % Favored : 78.76 % 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: -1.97 (0.18), residues: 1992 helix: 1.50 (0.25), residues: 432 sheet: -1.94 (0.18), residues: 645 loop : -2.19 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 314 HIS 0.006 0.001 HIS A 317 PHE 0.011 0.001 PHE K 91 TYR 0.027 0.002 TYR B 86 ARG 0.001 0.000 ARG B 507 *********************** 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 237 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 176 time to evaluate : 1.662 Fit side-chains REVERT: D 13 LYS cc_start: 0.8031 (mtpp) cc_final: 0.7600 (mtpp) REVERT: D 81 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7655 (tp) REVERT: F 42 LYS cc_start: 0.8333 (mptt) cc_final: 0.7855 (mtmt) REVERT: A 486 ASP cc_start: 0.7087 (p0) cc_final: 0.6532 (p0) REVERT: C 95 LEU cc_start: 0.8669 (mm) cc_final: 0.8455 (mm) REVERT: C 289 MET cc_start: 0.8957 (tpt) cc_final: 0.8088 (tpt) outliers start: 61 outliers final: 49 residues processed: 213 average time/residue: 0.2881 time to fit residues: 92.4454 Evaluate side-chains 218 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 168 time to evaluate : 1.909 ------------------------------------------------------------------------------- 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 4 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 20 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16035 Z= 0.350 Angle : 0.648 10.778 21729 Z= 0.333 Chirality : 0.046 0.159 2520 Planarity : 0.004 0.039 2736 Dihedral : 7.877 78.466 2205 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.79 % Allowed : 18.00 % 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: -1.98 (0.18), residues: 1992 helix: 1.34 (0.24), residues: 432 sheet: -1.89 (0.19), residues: 657 loop : -2.15 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 314 HIS 0.007 0.002 HIS B 317 PHE 0.015 0.002 PHE K 91 TYR 0.033 0.002 TYR C 86 ARG 0.002 0.000 ARG D 98 *********************** 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 239 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 171 time to evaluate : 3.320 Fit side-chains REVERT: D 13 LYS cc_start: 0.8042 (mtpp) cc_final: 0.7550 (mtpp) REVERT: D 81 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7555 (tp) REVERT: F 42 LYS cc_start: 0.8339 (mptt) cc_final: 0.7849 (mtmt) REVERT: A 486 ASP cc_start: 0.7114 (p0) cc_final: 0.6567 (p0) REVERT: C 289 MET cc_start: 0.8982 (tpt) cc_final: 0.8146 (tpt) outliers start: 68 outliers final: 55 residues processed: 215 average time/residue: 0.3272 time to fit residues: 107.2464 Evaluate side-chains 219 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 163 time to evaluate : 1.877 ------------------------------------------------------------------------------- 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 4 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 296 VAL 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 72 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 187 VAL 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 405 SER Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 11 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 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 158 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 K 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16035 Z= 0.197 Angle : 0.581 8.824 21729 Z= 0.298 Chirality : 0.043 0.190 2520 Planarity : 0.004 0.042 2736 Dihedral : 7.541 76.081 2205 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.01 % Allowed : 18.78 % 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: -1.64 (0.19), residues: 1992 helix: 1.66 (0.25), residues: 432 sheet: -1.74 (0.19), residues: 669 loop : -1.91 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 314 HIS 0.004 0.001 HIS A 317 PHE 0.010 0.001 PHE D 70 TYR 0.027 0.002 TYR C 86 ARG 0.001 0.000 ARG A 507 *********************** 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 239 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 185 time to evaluate : 2.086 Fit side-chains revert: symmetry clash REVERT: D 13 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7554 (mtpp) REVERT: D 81 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7670 (tp) REVERT: F 42 LYS cc_start: 0.8359 (mptt) cc_final: 0.7870 (mtmt) REVERT: A 344 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.6747 (t0) REVERT: A 486 ASP cc_start: 0.7050 (p0) cc_final: 0.6496 (p0) REVERT: C 289 MET cc_start: 0.8948 (tpt) cc_final: 0.8147 (tpt) outliers start: 54 outliers final: 41 residues processed: 212 average time/residue: 0.2856 time to fit residues: 90.9732 Evaluate side-chains 218 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain E residue 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 72 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 20 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 C residue 58 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 296 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 180 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 158 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 174 optimal weight: 0.6980 chunk 115 optimal weight: 0.0980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16035 Z= 0.186 Angle : 0.564 7.766 21729 Z= 0.288 Chirality : 0.043 0.194 2520 Planarity : 0.003 0.040 2736 Dihedral : 7.229 72.340 2205 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.84 % Allowed : 19.18 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.19), residues: 1992 helix: 1.85 (0.25), residues: 432 sheet: -1.52 (0.19), residues: 636 loop : -1.87 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 314 HIS 0.004 0.001 HIS B 317 PHE 0.010 0.001 PHE G 70 TYR 0.028 0.002 TYR B 86 ARG 0.001 0.000 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 192 time to evaluate : 1.854 Fit side-chains REVERT: D 13 LYS cc_start: 0.7954 (mtpp) cc_final: 0.7507 (mtpp) REVERT: D 81 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7615 (tp) REVERT: F 42 LYS cc_start: 0.8340 (mptt) cc_final: 0.7899 (mtmt) REVERT: F 52 LYS cc_start: 0.8306 (mttt) cc_final: 0.7924 (mmtt) REVERT: A 486 ASP cc_start: 0.6986 (p0) cc_final: 0.6456 (p0) REVERT: H 42 LYS cc_start: 0.8310 (mptt) cc_final: 0.7890 (mtmt) REVERT: C 289 MET cc_start: 0.8972 (tpt) cc_final: 0.8155 (tpt) outliers start: 51 outliers final: 45 residues processed: 219 average time/residue: 0.2982 time to fit residues: 98.2111 Evaluate side-chains 220 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 174 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL 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 F residue 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain H residue 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 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 405 SER Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 20 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 C residue 58 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 425 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 122 optimal weight: 0.0070 overall best weight: 1.2004 ------------------------------------------------------------------------------- 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 G 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 0.004 0.059 16035 Z= 0.243 Angle : 0.601 8.651 21729 Z= 0.306 Chirality : 0.044 0.192 2520 Planarity : 0.003 0.039 2736 Dihedral : 7.235 70.065 2205 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.01 % Allowed : 19.23 % Favored : 77.76 % 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: -1.43 (0.19), residues: 1992 helix: 1.71 (0.25), residues: 432 sheet: -1.47 (0.19), residues: 639 loop : -1.85 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 314 HIS 0.005 0.001 HIS A 317 PHE 0.011 0.001 PHE F 91 TYR 0.031 0.002 TYR B 86 ARG 0.001 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 234 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 180 time to evaluate : 1.781 Fit side-chains REVERT: D 13 LYS cc_start: 0.7993 (mtpp) cc_final: 0.7544 (mtpp) REVERT: D 81 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7601 (tp) REVERT: F 42 LYS cc_start: 0.8352 (mptt) cc_final: 0.7880 (mtmt) REVERT: A 344 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.6676 (t0) REVERT: A 486 ASP cc_start: 0.6998 (p0) cc_final: 0.6427 (p0) REVERT: H 42 LYS cc_start: 0.8301 (mptt) cc_final: 0.7872 (mtmt) REVERT: C 289 MET cc_start: 0.8984 (tpt) cc_final: 0.8178 (tpt) outliers start: 54 outliers final: 50 residues processed: 208 average time/residue: 0.3017 time to fit residues: 94.3114 Evaluate side-chains 225 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 173 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL 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 F residue 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 158 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 393 CYS Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 425 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 20 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 158 LEU Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 425 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.137315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.108931 restraints weight = 22557.623| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.19 r_work: 0.3218 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16035 Z= 0.261 Angle : 0.607 9.714 21729 Z= 0.309 Chirality : 0.044 0.196 2520 Planarity : 0.003 0.039 2736 Dihedral : 7.226 69.226 2205 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.23 % Allowed : 19.06 % Favored : 77.70 % 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: -1.40 (0.19), residues: 1992 helix: 1.67 (0.25), residues: 432 sheet: -1.46 (0.19), residues: 663 loop : -1.78 (0.20), residues: 897 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 0.012 0.001 PHE K 91 TYR 0.030 0.002 TYR B 86 ARG 0.001 0.000 ARG D 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3604.31 seconds wall clock time: 68 minutes 0.20 seconds (4080.20 seconds total)