Starting phenix.real_space_refine on Thu Feb 15 07:48:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x54_33007/02_2024/7x54_33007_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x54_33007/02_2024/7x54_33007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x54_33007/02_2024/7x54_33007.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x54_33007/02_2024/7x54_33007.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x54_33007/02_2024/7x54_33007_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x54_33007/02_2024/7x54_33007_updated.pdb" } resolution = 3.9 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 40 5.16 5 C 7370 2.51 5 N 1900 2.21 5 O 2250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11575 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2287 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 5, 'TRANS': 279} Chain: "B" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2287 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 5, 'TRANS': 279} Chain: "C" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2287 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 5, 'TRANS': 279} Chain: "D" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2287 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 5, 'TRANS': 279} Chain: "E" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2287 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 5, 'TRANS': 279} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.87, per 1000 atoms: 0.51 Number of scatterers: 11575 At special positions: 0 Unit cell: (80.04, 97.44, 160.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 10 15.00 Mg 5 11.99 O 2250 8.00 N 1900 7.00 C 7370 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.56 Conformation dependent library (CDL) restraints added in 2.2 seconds 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2670 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 15 sheets defined 33.7% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 68 through 77 Processing helix chain 'A' and resid 96 through 106 removed outlier: 3.778A pdb=" N ILE A 103 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU A 104 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 removed outlier: 4.275A pdb=" N TYR A 138 " --> pdb=" O TYR A 134 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 134 through 139' Processing helix chain 'A' and resid 142 through 145 No H-bonds generated for 'chain 'A' and resid 142 through 145' Processing helix chain 'A' and resid 179 through 193 removed outlier: 3.597A pdb=" N LEU A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 215 through 228 removed outlier: 3.542A pdb=" N ILE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 251 through 256 removed outlier: 4.381A pdb=" N LYS A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 283 removed outlier: 4.067A pdb=" N ASN A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 276 " --> pdb=" O ASN A 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 63 No H-bonds generated for 'chain 'B' and resid 61 through 63' Processing helix chain 'B' and resid 68 through 77 Processing helix chain 'B' and resid 96 through 106 removed outlier: 3.780A pdb=" N ILE B 103 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU B 104 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 139 removed outlier: 4.276A pdb=" N TYR B 138 " --> pdb=" O TYR B 134 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 134 through 139' Processing helix chain 'B' and resid 142 through 145 No H-bonds generated for 'chain 'B' and resid 142 through 145' Processing helix chain 'B' and resid 179 through 193 removed outlier: 3.598A pdb=" N LEU B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 215 through 228 removed outlier: 3.541A pdb=" N ILE B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 249 Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.381A pdb=" N LYS B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 283 removed outlier: 4.067A pdb=" N ASN B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 276 " --> pdb=" O ASN B 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 63 No H-bonds generated for 'chain 'C' and resid 61 through 63' Processing helix chain 'C' and resid 68 through 77 Processing helix chain 'C' and resid 96 through 106 removed outlier: 3.779A pdb=" N ILE C 103 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU C 104 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 139 removed outlier: 4.275A pdb=" N TYR C 138 " --> pdb=" O TYR C 134 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 134 through 139' Processing helix chain 'C' and resid 142 through 145 No H-bonds generated for 'chain 'C' and resid 142 through 145' Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.597A pdb=" N LEU C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 208 Processing helix chain 'C' and resid 215 through 228 removed outlier: 3.541A pdb=" N ILE C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 249 Processing helix chain 'C' and resid 251 through 256 removed outlier: 4.381A pdb=" N LYS C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 283 removed outlier: 4.067A pdb=" N ASN C 272 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 276 " --> pdb=" O ASN C 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' Processing helix chain 'D' and resid 68 through 77 Processing helix chain 'D' and resid 96 through 106 removed outlier: 3.779A pdb=" N ILE D 103 " --> pdb=" O THR D 100 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU D 104 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 139 removed outlier: 4.276A pdb=" N TYR D 138 " --> pdb=" O TYR D 134 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 134 through 139' Processing helix chain 'D' and resid 142 through 145 No H-bonds generated for 'chain 'D' and resid 142 through 145' Processing helix chain 'D' and resid 179 through 193 removed outlier: 3.598A pdb=" N LEU D 189 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA D 192 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS D 193 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 208 Processing helix chain 'D' and resid 215 through 228 removed outlier: 3.541A pdb=" N ILE D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 249 Processing helix chain 'D' and resid 251 through 256 removed outlier: 4.381A pdb=" N LYS D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 283 removed outlier: 4.066A pdb=" N ASN D 272 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N VAL D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA D 276 " --> pdb=" O ASN D 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 63 No H-bonds generated for 'chain 'E' and resid 61 through 63' Processing helix chain 'E' and resid 68 through 77 Processing helix chain 'E' and resid 96 through 106 removed outlier: 3.779A pdb=" N ILE E 103 " --> pdb=" O THR E 100 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU E 104 " --> pdb=" O ARG E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 4.276A pdb=" N TYR E 138 " --> pdb=" O TYR E 134 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 134 through 139' Processing helix chain 'E' and resid 142 through 145 No H-bonds generated for 'chain 'E' and resid 142 through 145' Processing helix chain 'E' and resid 179 through 193 removed outlier: 3.597A pdb=" N LEU E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA E 192 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 208 Processing helix chain 'E' and resid 215 through 228 removed outlier: 3.541A pdb=" N ILE E 219 " --> pdb=" O SER E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 249 Processing helix chain 'E' and resid 251 through 256 removed outlier: 4.381A pdb=" N LYS E 256 " --> pdb=" O GLU E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 283 removed outlier: 4.068A pdb=" N ASN E 272 " --> pdb=" O ALA E 268 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N VAL E 273 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA E 276 " --> pdb=" O ASN E 272 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 20 through 24 removed outlier: 4.208A pdb=" N LYS A 2 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 6 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 90 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N ILE A 85 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LYS A 123 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU A 87 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ASN A 125 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 12.505A pdb=" N LEU A 89 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N LEU A 127 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 11.646A pdb=" N LEU A 91 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N VAL A 129 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 39 through 43 removed outlier: 4.633A pdb=" N GLN A 39 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 262 through 264 removed outlier: 6.004A pdb=" N THR A 240 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS A 171 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLU A 165 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE A 169 " --> pdb=" O GLU A 165 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 20 through 24 removed outlier: 4.208A pdb=" N LYS B 2 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 6 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 90 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N ILE B 85 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LYS B 123 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU B 87 " --> pdb=" O LYS B 123 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ASN B 125 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 12.505A pdb=" N LEU B 89 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 9.954A pdb=" N LEU B 127 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 11.648A pdb=" N LEU B 91 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N VAL B 129 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 39 through 43 removed outlier: 4.632A pdb=" N GLN B 39 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 262 through 264 removed outlier: 6.003A pdb=" N THR B 240 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 171 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLU B 165 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 20 through 24 removed outlier: 4.208A pdb=" N LYS C 2 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 6 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 90 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N ILE C 85 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LYS C 123 " --> pdb=" O ILE C 85 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU C 87 " --> pdb=" O LYS C 123 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ASN C 125 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 12.503A pdb=" N LEU C 89 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N LEU C 127 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 11.648A pdb=" N LEU C 91 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N VAL C 129 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 39 through 43 removed outlier: 4.633A pdb=" N GLN C 39 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 262 through 264 removed outlier: 6.004A pdb=" N THR C 240 " --> pdb=" O LYS C 263 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS C 171 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLU C 165 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE C 169 " --> pdb=" O GLU C 165 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 20 through 24 removed outlier: 4.207A pdb=" N LYS D 2 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 6 " --> pdb=" O THR D 88 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D 90 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N ILE D 85 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LYS D 123 " --> pdb=" O ILE D 85 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU D 87 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ASN D 125 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 12.505A pdb=" N LEU D 89 " --> pdb=" O ASN D 125 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N LEU D 127 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 11.647A pdb=" N LEU D 91 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N VAL D 129 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 39 through 43 removed outlier: 4.632A pdb=" N GLN D 39 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 262 through 264 removed outlier: 6.004A pdb=" N THR D 240 " --> pdb=" O LYS D 263 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS D 171 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLU D 165 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 20 through 24 removed outlier: 4.208A pdb=" N LYS E 2 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL E 6 " --> pdb=" O THR E 88 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU E 90 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N ILE E 85 " --> pdb=" O GLU E 121 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LYS E 123 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU E 87 " --> pdb=" O LYS E 123 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ASN E 125 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 12.505A pdb=" N LEU E 89 " --> pdb=" O ASN E 125 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N LEU E 127 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 11.647A pdb=" N LEU E 91 " --> pdb=" O LEU E 127 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N VAL E 129 " --> pdb=" O LEU E 91 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 39 through 43 removed outlier: 4.633A pdb=" N GLN E 39 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 262 through 264 removed outlier: 6.003A pdb=" N THR E 240 " --> pdb=" O LYS E 263 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS E 171 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLU E 165 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1035 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: 3.07 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3665 1.34 - 1.46: 2469 1.46 - 1.58: 5531 1.58 - 1.69: 15 1.69 - 1.81: 70 Bond restraints: 11750 Sorted by residual: bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.76e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.75e+00 ... (remaining 11745 not shown) Histogram of bond angle deviations from ideal: 97.50 - 105.23: 110 105.23 - 112.97: 6397 112.97 - 120.70: 5174 120.70 - 128.44: 4124 128.44 - 136.17: 35 Bond angle restraints: 15840 Sorted by residual: angle pdb=" CA MET A 277 " pdb=" CB MET A 277 " pdb=" CG MET A 277 " ideal model delta sigma weight residual 114.10 119.36 -5.26 2.00e+00 2.50e-01 6.91e+00 angle pdb=" CA MET B 277 " pdb=" CB MET B 277 " pdb=" CG MET B 277 " ideal model delta sigma weight residual 114.10 119.33 -5.23 2.00e+00 2.50e-01 6.85e+00 angle pdb=" CA MET D 277 " pdb=" CB MET D 277 " pdb=" CG MET D 277 " ideal model delta sigma weight residual 114.10 119.33 -5.23 2.00e+00 2.50e-01 6.85e+00 angle pdb=" CA MET C 277 " pdb=" CB MET C 277 " pdb=" CG MET C 277 " ideal model delta sigma weight residual 114.10 119.32 -5.22 2.00e+00 2.50e-01 6.80e+00 angle pdb=" CA MET E 277 " pdb=" CB MET E 277 " pdb=" CG MET E 277 " ideal model delta sigma weight residual 114.10 119.28 -5.18 2.00e+00 2.50e-01 6.72e+00 ... (remaining 15835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.05: 6969 31.05 - 62.11: 156 62.11 - 93.16: 15 93.16 - 124.22: 5 124.22 - 155.27: 10 Dihedral angle restraints: 7155 sinusoidal: 2985 harmonic: 4170 Sorted by residual: dihedral pdb=" C5' ADP B 300 " pdb=" O5' ADP B 300 " pdb=" PA ADP B 300 " pdb=" O2A ADP B 300 " ideal model delta sinusoidal sigma weight residual -60.00 95.27 -155.27 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" C5' ADP E 300 " pdb=" O5' ADP E 300 " pdb=" PA ADP E 300 " pdb=" O2A ADP E 300 " ideal model delta sinusoidal sigma weight residual -60.00 95.27 -155.27 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" C5' ADP C 300 " pdb=" O5' ADP C 300 " pdb=" PA ADP C 300 " pdb=" O2A ADP C 300 " ideal model delta sinusoidal sigma weight residual -60.00 95.26 -155.26 1 2.00e+01 2.50e-03 4.58e+01 ... (remaining 7152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1220 0.032 - 0.064: 374 0.064 - 0.097: 94 0.097 - 0.129: 88 0.129 - 0.161: 19 Chirality restraints: 1795 Sorted by residual: chirality pdb=" CB VAL A 5 " pdb=" CA VAL A 5 " pdb=" CG1 VAL A 5 " pdb=" CG2 VAL A 5 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CB VAL B 5 " pdb=" CA VAL B 5 " pdb=" CG1 VAL B 5 " pdb=" CG2 VAL B 5 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CB VAL C 5 " pdb=" CA VAL C 5 " pdb=" CG1 VAL C 5 " pdb=" CG2 VAL C 5 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.32e-01 ... (remaining 1792 not shown) Planarity restraints: 1980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 253 " -0.014 2.00e-02 2.50e+03 1.47e-02 4.33e+00 pdb=" CG TYR B 253 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR B 253 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 253 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 253 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 253 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 253 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 253 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 253 " 0.014 2.00e-02 2.50e+03 1.46e-02 4.29e+00 pdb=" CG TYR C 253 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR C 253 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR C 253 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR C 253 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR C 253 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 253 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 253 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 253 " -0.014 2.00e-02 2.50e+03 1.45e-02 4.22e+00 pdb=" CG TYR D 253 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR D 253 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR D 253 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR D 253 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR D 253 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 253 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 253 " -0.002 2.00e-02 2.50e+03 ... (remaining 1977 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 387 2.68 - 3.23: 12344 3.23 - 3.79: 16793 3.79 - 4.34: 24457 4.34 - 4.90: 40066 Nonbonded interactions: 94047 Sorted by model distance: nonbonded pdb=" O3B ADP E 300 " pdb="MG MG E 301 " model vdw 2.121 2.170 nonbonded pdb=" O3B ADP A 300 " pdb="MG MG A 301 " model vdw 2.122 2.170 nonbonded pdb=" O3B ADP C 300 " pdb="MG MG C 301 " model vdw 2.122 2.170 nonbonded pdb=" O3B ADP B 300 " pdb="MG MG B 301 " model vdw 2.122 2.170 nonbonded pdb=" O3B ADP D 300 " pdb="MG MG D 301 " model vdw 2.122 2.170 ... (remaining 94042 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.800 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: 11.630 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 32.710 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 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 : 0.003 0.032 11750 Z= 0.171 Angle : 0.611 6.718 15840 Z= 0.309 Chirality : 0.042 0.161 1795 Planarity : 0.003 0.045 1980 Dihedral : 15.234 155.270 4485 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 0.39 % Allowed : 0.47 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1415 helix: -0.21 (0.26), residues: 365 sheet: -1.53 (0.29), residues: 295 loop : -1.31 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 284 HIS 0.001 0.000 HIS A 265 PHE 0.004 0.001 PHE D 59 TYR 0.035 0.002 TYR B 253 ARG 0.002 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 322 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.7865 (mmm) cc_final: 0.7648 (mmp) REVERT: A 148 ASP cc_start: 0.7242 (p0) cc_final: 0.6901 (p0) REVERT: A 202 ILE cc_start: 0.7642 (tt) cc_final: 0.7121 (mt) REVERT: A 251 LYS cc_start: 0.7934 (ptmm) cc_final: 0.7545 (ttpp) REVERT: A 274 ASP cc_start: 0.8738 (m-30) cc_final: 0.8405 (m-30) REVERT: B 14 LYS cc_start: 0.8568 (mtmm) cc_final: 0.8117 (mtmm) REVERT: B 39 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8012 (mm-40) REVERT: B 196 ASP cc_start: 0.7318 (p0) cc_final: 0.7001 (p0) REVERT: C 2 LYS cc_start: 0.8054 (mmtt) cc_final: 0.7813 (mmtt) REVERT: C 39 GLN cc_start: 0.8362 (mm-40) cc_final: 0.7960 (mm-40) REVERT: C 255 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8302 (mm-30) REVERT: D 14 LYS cc_start: 0.8938 (mtmm) cc_final: 0.8614 (mtmm) REVERT: D 39 GLN cc_start: 0.8428 (mm-40) cc_final: 0.7962 (mm-40) REVERT: E 39 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8162 (mm-40) REVERT: E 196 ASP cc_start: 0.7604 (p0) cc_final: 0.7382 (p0) REVERT: E 202 ILE cc_start: 0.8570 (tt) cc_final: 0.8242 (mt) REVERT: E 270 THR cc_start: 0.8318 (p) cc_final: 0.7932 (m) outliers start: 5 outliers final: 2 residues processed: 322 average time/residue: 0.2633 time to fit residues: 116.7302 Evaluate side-chains 184 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 182 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain B residue 277 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN B 69 GLN C 69 GLN D 69 GLN D 191 ASN D 267 ASN E 60 ASN E 69 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 11750 Z= 0.448 Angle : 0.801 7.873 15840 Z= 0.403 Chirality : 0.051 0.172 1795 Planarity : 0.004 0.054 1980 Dihedral : 13.330 172.443 1601 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.75 % Allowed : 11.61 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.27 (0.23), residues: 1415 helix: -0.02 (0.27), residues: 355 sheet: -0.96 (0.29), residues: 370 loop : -1.14 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 284 HIS 0.004 0.001 HIS C 265 PHE 0.030 0.002 PHE D 59 TYR 0.019 0.002 TYR D 253 ARG 0.007 0.001 ARG E 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 207 time to evaluate : 1.378 Fit side-chains REVERT: A 55 LEU cc_start: 0.8616 (tp) cc_final: 0.8291 (tp) REVERT: A 65 ASP cc_start: 0.8157 (t0) cc_final: 0.7762 (t0) REVERT: A 111 PHE cc_start: 0.7854 (m-10) cc_final: 0.6191 (m-10) REVERT: A 169 ILE cc_start: 0.9244 (mp) cc_final: 0.8710 (tt) REVERT: A 232 TYR cc_start: 0.8878 (m-10) cc_final: 0.8571 (m-10) REVERT: B 19 ASN cc_start: 0.8308 (m-40) cc_final: 0.7987 (p0) REVERT: B 39 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8118 (mm-40) REVERT: B 65 ASP cc_start: 0.7600 (t0) cc_final: 0.7339 (t0) REVERT: B 196 ASP cc_start: 0.8017 (p0) cc_final: 0.7781 (p0) REVERT: B 277 MET cc_start: 0.8334 (tmm) cc_final: 0.7947 (tmm) REVERT: C 19 ASN cc_start: 0.8588 (m-40) cc_final: 0.7982 (p0) REVERT: C 39 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8120 (mm-40) REVERT: C 65 ASP cc_start: 0.7583 (t70) cc_final: 0.7304 (t0) REVERT: D 19 ASN cc_start: 0.8416 (m-40) cc_final: 0.8086 (p0) REVERT: D 39 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8412 (mm-40) REVERT: D 40 ARG cc_start: 0.8115 (ptt-90) cc_final: 0.7780 (ptp90) REVERT: D 61 LYS cc_start: 0.8090 (pttt) cc_final: 0.7727 (pttp) REVERT: D 248 LEU cc_start: 0.8906 (mm) cc_final: 0.8528 (tt) REVERT: D 267 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.8164 (p0) REVERT: E 39 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8276 (mm-40) REVERT: E 248 LEU cc_start: 0.8626 (mm) cc_final: 0.8278 (tt) outliers start: 35 outliers final: 27 residues processed: 234 average time/residue: 0.2476 time to fit residues: 83.1252 Evaluate side-chains 192 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 164 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 267 ASN Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 246 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 chunk 137 optimal weight: 0.4980 chunk 113 optimal weight: 0.6980 chunk 126 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN D 267 ASN E 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11750 Z= 0.202 Angle : 0.633 9.975 15840 Z= 0.312 Chirality : 0.044 0.156 1795 Planarity : 0.003 0.048 1980 Dihedral : 11.988 169.457 1595 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.98 % Allowed : 13.96 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.24), residues: 1415 helix: 0.56 (0.28), residues: 370 sheet: -0.64 (0.29), residues: 370 loop : -0.98 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 284 HIS 0.001 0.001 HIS D 265 PHE 0.008 0.001 PHE D 59 TYR 0.019 0.001 TYR A 72 ARG 0.004 0.001 ARG E 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 216 time to evaluate : 1.344 Fit side-chains revert: symmetry clash REVERT: A 19 ASN cc_start: 0.8446 (m-40) cc_final: 0.8186 (p0) REVERT: A 65 ASP cc_start: 0.8093 (t0) cc_final: 0.7736 (t0) REVERT: A 132 GLU cc_start: 0.7404 (tp30) cc_final: 0.7174 (tp30) REVERT: A 148 ASP cc_start: 0.7469 (p0) cc_final: 0.6914 (p0) REVERT: A 169 ILE cc_start: 0.9246 (mp) cc_final: 0.8783 (tt) REVERT: A 199 GLU cc_start: 0.7827 (mp0) cc_final: 0.7615 (mp0) REVERT: A 202 ILE cc_start: 0.8199 (tt) cc_final: 0.7836 (mt) REVERT: A 274 ASP cc_start: 0.8476 (m-30) cc_final: 0.8109 (m-30) REVERT: A 277 MET cc_start: 0.8323 (tmm) cc_final: 0.8114 (tmm) REVERT: B 19 ASN cc_start: 0.8324 (m-40) cc_final: 0.8098 (p0) REVERT: B 39 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8206 (mm-40) REVERT: B 64 ARG cc_start: 0.7687 (ptt90) cc_final: 0.7195 (ptt-90) REVERT: B 65 ASP cc_start: 0.7590 (t0) cc_final: 0.7302 (t0) REVERT: B 132 GLU cc_start: 0.8043 (tp30) cc_final: 0.7563 (tp30) REVERT: B 196 ASP cc_start: 0.8004 (p0) cc_final: 0.7692 (p0) REVERT: B 202 ILE cc_start: 0.8865 (tt) cc_final: 0.8605 (tp) REVERT: C 19 ASN cc_start: 0.8601 (m-40) cc_final: 0.8044 (p0) REVERT: C 39 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8096 (mm-40) REVERT: C 65 ASP cc_start: 0.7493 (t70) cc_final: 0.7149 (t0) REVERT: C 132 GLU cc_start: 0.8255 (tp30) cc_final: 0.7664 (tp30) REVERT: D 19 ASN cc_start: 0.8368 (m-40) cc_final: 0.8115 (p0) REVERT: D 39 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8333 (mm-40) REVERT: D 40 ARG cc_start: 0.7932 (ptt-90) cc_final: 0.7682 (ptp90) REVERT: D 132 GLU cc_start: 0.7843 (tp30) cc_final: 0.7578 (tp30) REVERT: D 143 GLU cc_start: 0.8548 (tp30) cc_final: 0.8234 (tp30) REVERT: D 241 ILE cc_start: 0.9115 (mm) cc_final: 0.8897 (mm) REVERT: D 248 LEU cc_start: 0.8786 (mm) cc_final: 0.8503 (tt) REVERT: D 277 MET cc_start: 0.8344 (tpp) cc_final: 0.8054 (tpp) REVERT: E 39 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8389 (mm-40) REVERT: E 248 LEU cc_start: 0.8485 (mm) cc_final: 0.8123 (tt) outliers start: 38 outliers final: 27 residues processed: 244 average time/residue: 0.2204 time to fit residues: 78.0492 Evaluate side-chains 212 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 185 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 246 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 135 optimal weight: 20.0000 chunk 121 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN B 86 ASN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN E 267 ASN E 272 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11750 Z= 0.295 Angle : 0.674 6.805 15840 Z= 0.333 Chirality : 0.046 0.146 1795 Planarity : 0.004 0.053 1980 Dihedral : 11.225 126.646 1595 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 3.92 % Allowed : 15.61 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.23), residues: 1415 helix: 0.78 (0.28), residues: 355 sheet: -0.62 (0.29), residues: 370 loop : -1.10 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 284 HIS 0.002 0.001 HIS C 265 PHE 0.018 0.002 PHE D 59 TYR 0.016 0.002 TYR A 134 ARG 0.007 0.001 ARG C 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 198 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASN cc_start: 0.8469 (m-40) cc_final: 0.8241 (p0) REVERT: A 55 LEU cc_start: 0.8732 (tp) cc_final: 0.8513 (tp) REVERT: A 65 ASP cc_start: 0.8190 (t0) cc_final: 0.7892 (t0) REVERT: A 110 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.8162 (p0) REVERT: A 132 GLU cc_start: 0.7540 (tp30) cc_final: 0.7262 (tp30) REVERT: A 148 ASP cc_start: 0.7499 (p0) cc_final: 0.6890 (p0) REVERT: A 169 ILE cc_start: 0.9293 (mp) cc_final: 0.8861 (tt) REVERT: A 214 ASP cc_start: 0.8068 (m-30) cc_final: 0.7673 (m-30) REVERT: A 277 MET cc_start: 0.8191 (tmm) cc_final: 0.7972 (tmm) REVERT: B 19 ASN cc_start: 0.8352 (m-40) cc_final: 0.8109 (p0) REVERT: B 39 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8234 (mm-40) REVERT: B 64 ARG cc_start: 0.7812 (ptt90) cc_final: 0.7392 (ptt-90) REVERT: B 65 ASP cc_start: 0.7668 (t0) cc_final: 0.7350 (t0) REVERT: B 169 ILE cc_start: 0.9097 (mt) cc_final: 0.8626 (tt) REVERT: B 196 ASP cc_start: 0.8011 (p0) cc_final: 0.7656 (p0) REVERT: C 39 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8136 (mm-40) REVERT: C 65 ASP cc_start: 0.7502 (t70) cc_final: 0.7101 (t0) REVERT: C 132 GLU cc_start: 0.8361 (tp30) cc_final: 0.8115 (tp30) REVERT: D 19 ASN cc_start: 0.8355 (m-40) cc_final: 0.8058 (p0) REVERT: D 40 ARG cc_start: 0.8061 (ptt-90) cc_final: 0.7751 (ptp90) REVERT: D 132 GLU cc_start: 0.8050 (tp30) cc_final: 0.7842 (tp30) REVERT: D 166 ASN cc_start: 0.8570 (p0) cc_final: 0.8272 (p0) REVERT: D 248 LEU cc_start: 0.8913 (mm) cc_final: 0.8596 (tt) REVERT: E 248 LEU cc_start: 0.8652 (mm) cc_final: 0.8291 (tt) outliers start: 50 outliers final: 33 residues processed: 238 average time/residue: 0.2247 time to fit residues: 78.2507 Evaluate side-chains 205 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 171 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 246 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.8980 chunk 1 optimal weight: 0.2980 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11750 Z= 0.199 Angle : 0.632 8.213 15840 Z= 0.310 Chirality : 0.044 0.156 1795 Planarity : 0.003 0.051 1980 Dihedral : 10.774 124.848 1595 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.29 % Allowed : 18.51 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.23), residues: 1415 helix: 1.01 (0.28), residues: 360 sheet: -0.44 (0.29), residues: 365 loop : -1.08 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 284 HIS 0.001 0.001 HIS C 265 PHE 0.008 0.001 PHE A 23 TYR 0.023 0.001 TYR A 72 ARG 0.005 0.001 ARG C 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 213 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASN cc_start: 0.8492 (m-40) cc_final: 0.8227 (p0) REVERT: A 65 ASP cc_start: 0.8115 (t0) cc_final: 0.7720 (t0) REVERT: A 76 LYS cc_start: 0.8610 (mtpp) cc_final: 0.8379 (mtpp) REVERT: A 110 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8138 (p0) REVERT: A 132 GLU cc_start: 0.7408 (tp30) cc_final: 0.7184 (tp30) REVERT: A 148 ASP cc_start: 0.7522 (p0) cc_final: 0.6892 (p0) REVERT: A 169 ILE cc_start: 0.9228 (mp) cc_final: 0.8842 (tp) REVERT: A 214 ASP cc_start: 0.8009 (m-30) cc_final: 0.7633 (m-30) REVERT: A 241 ILE cc_start: 0.9164 (mm) cc_final: 0.8818 (mm) REVERT: A 277 MET cc_start: 0.8116 (tmm) cc_final: 0.7916 (tmm) REVERT: B 19 ASN cc_start: 0.8415 (m-40) cc_final: 0.8147 (p0) REVERT: B 39 GLN cc_start: 0.8539 (mm-40) cc_final: 0.8259 (mm-40) REVERT: B 64 ARG cc_start: 0.7648 (ptt90) cc_final: 0.7185 (ptt-90) REVERT: B 65 ASP cc_start: 0.7637 (t0) cc_final: 0.7327 (t0) REVERT: B 132 GLU cc_start: 0.8020 (tp30) cc_final: 0.7142 (tp30) REVERT: B 169 ILE cc_start: 0.9091 (mt) cc_final: 0.8593 (tt) REVERT: B 202 ILE cc_start: 0.8845 (tt) cc_final: 0.8592 (tp) REVERT: C 19 ASN cc_start: 0.8591 (m-40) cc_final: 0.8007 (p0) REVERT: C 39 GLN cc_start: 0.8357 (mm-40) cc_final: 0.8061 (mm-40) REVERT: C 65 ASP cc_start: 0.7424 (t70) cc_final: 0.7106 (t0) REVERT: C 132 GLU cc_start: 0.8375 (tp30) cc_final: 0.7991 (tp30) REVERT: C 196 ASP cc_start: 0.7941 (p0) cc_final: 0.7732 (p0) REVERT: D 19 ASN cc_start: 0.8353 (m-40) cc_final: 0.8109 (p0) REVERT: D 40 ARG cc_start: 0.8077 (ptt-90) cc_final: 0.7762 (ptp90) REVERT: D 101 ARG cc_start: 0.8203 (mtm180) cc_final: 0.8002 (ptp-170) REVERT: D 166 ASN cc_start: 0.8543 (p0) cc_final: 0.8223 (p0) REVERT: D 248 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8567 (tt) REVERT: E 64 ARG cc_start: 0.8144 (ptt90) cc_final: 0.7819 (ptt-90) REVERT: E 96 MET cc_start: 0.5784 (mmp) cc_final: 0.5532 (mmp) REVERT: E 248 LEU cc_start: 0.8509 (mm) cc_final: 0.8153 (tt) REVERT: E 272 ASN cc_start: 0.7979 (m-40) cc_final: 0.7716 (m110) outliers start: 42 outliers final: 32 residues processed: 245 average time/residue: 0.2208 time to fit residues: 78.8296 Evaluate side-chains 224 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 190 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain E residue 246 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 79 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 135 optimal weight: 50.0000 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 11 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11750 Z= 0.197 Angle : 0.632 7.558 15840 Z= 0.308 Chirality : 0.044 0.182 1795 Planarity : 0.003 0.046 1980 Dihedral : 10.449 129.546 1595 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 3.53 % Allowed : 18.67 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.23), residues: 1415 helix: 1.13 (0.29), residues: 360 sheet: -0.42 (0.29), residues: 365 loop : -0.98 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 284 HIS 0.002 0.001 HIS C 265 PHE 0.009 0.001 PHE A 23 TYR 0.019 0.001 TYR A 137 ARG 0.006 0.001 ARG C 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 209 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASN cc_start: 0.8429 (m-40) cc_final: 0.8211 (p0) REVERT: A 65 ASP cc_start: 0.8132 (t0) cc_final: 0.7707 (t0) REVERT: A 76 LYS cc_start: 0.8570 (mtpp) cc_final: 0.8338 (mtmt) REVERT: A 110 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.8161 (p0) REVERT: A 148 ASP cc_start: 0.7523 (p0) cc_final: 0.6916 (p0) REVERT: A 214 ASP cc_start: 0.7954 (m-30) cc_final: 0.7579 (m-30) REVERT: A 249 MET cc_start: 0.8462 (ttp) cc_final: 0.8137 (tmm) REVERT: B 19 ASN cc_start: 0.8400 (m-40) cc_final: 0.8135 (p0) REVERT: B 65 ASP cc_start: 0.7692 (t0) cc_final: 0.7373 (t0) REVERT: B 128 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7745 (tmm) REVERT: B 169 ILE cc_start: 0.9071 (mt) cc_final: 0.8572 (tt) REVERT: B 202 ILE cc_start: 0.8854 (tt) cc_final: 0.8607 (tp) REVERT: C 39 GLN cc_start: 0.8335 (mm-40) cc_final: 0.8085 (mm-40) REVERT: C 65 ASP cc_start: 0.7465 (t70) cc_final: 0.7177 (t0) REVERT: C 95 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7782 (mt0) REVERT: C 132 GLU cc_start: 0.8324 (tp30) cc_final: 0.7865 (tp30) REVERT: C 196 ASP cc_start: 0.7959 (p0) cc_final: 0.7742 (p0) REVERT: D 40 ARG cc_start: 0.8076 (ptt-90) cc_final: 0.7735 (ptp90) REVERT: D 95 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7456 (mp10) REVERT: D 128 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7570 (tmt) REVERT: D 166 ASN cc_start: 0.8588 (p0) cc_final: 0.8220 (p0) REVERT: D 248 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8564 (tt) REVERT: E 64 ARG cc_start: 0.8084 (ptt90) cc_final: 0.7717 (ptt-90) REVERT: E 248 LEU cc_start: 0.8526 (mm) cc_final: 0.8178 (tt) REVERT: E 272 ASN cc_start: 0.7995 (m-40) cc_final: 0.7754 (m110) outliers start: 45 outliers final: 31 residues processed: 241 average time/residue: 0.2121 time to fit residues: 75.0239 Evaluate side-chains 224 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 187 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain E residue 246 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.4980 chunk 77 optimal weight: 0.2980 chunk 98 optimal weight: 0.0870 chunk 76 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 0.3980 chunk 62 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11750 Z= 0.181 Angle : 0.641 8.677 15840 Z= 0.308 Chirality : 0.044 0.168 1795 Planarity : 0.003 0.049 1980 Dihedral : 9.945 136.693 1595 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.06 % Allowed : 20.00 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.23), residues: 1415 helix: 1.21 (0.29), residues: 360 sheet: -0.72 (0.27), residues: 390 loop : -0.92 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 284 HIS 0.002 0.001 HIS D 265 PHE 0.012 0.001 PHE C 38 TYR 0.019 0.001 TYR A 137 ARG 0.007 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 207 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8157 (t0) cc_final: 0.7765 (t0) REVERT: A 110 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.8146 (p0) REVERT: A 148 ASP cc_start: 0.7451 (p0) cc_final: 0.6916 (p0) REVERT: A 169 ILE cc_start: 0.9066 (mp) cc_final: 0.8580 (tt) REVERT: A 214 ASP cc_start: 0.7938 (m-30) cc_final: 0.7542 (m-30) REVERT: A 241 ILE cc_start: 0.9166 (mm) cc_final: 0.8847 (mm) REVERT: A 249 MET cc_start: 0.8467 (ttp) cc_final: 0.8111 (tmm) REVERT: B 19 ASN cc_start: 0.8361 (m-40) cc_final: 0.8105 (p0) REVERT: B 65 ASP cc_start: 0.7738 (t0) cc_final: 0.7448 (t0) REVERT: B 95 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7383 (mp10) REVERT: B 128 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7729 (tmm) REVERT: B 169 ILE cc_start: 0.9088 (mt) cc_final: 0.8573 (tt) REVERT: B 199 GLU cc_start: 0.7825 (mp0) cc_final: 0.7564 (mp0) REVERT: B 202 ILE cc_start: 0.8840 (tt) cc_final: 0.8632 (tp) REVERT: C 65 ASP cc_start: 0.7398 (t70) cc_final: 0.7144 (t0) REVERT: C 95 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7859 (mt0) REVERT: C 132 GLU cc_start: 0.8303 (tp30) cc_final: 0.7870 (tp30) REVERT: C 161 ILE cc_start: 0.9082 (mt) cc_final: 0.8875 (tp) REVERT: C 196 ASP cc_start: 0.7934 (p0) cc_final: 0.7691 (p0) REVERT: D 40 ARG cc_start: 0.8023 (ptt-90) cc_final: 0.7682 (ptp90) REVERT: D 248 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8551 (tt) REVERT: E 64 ARG cc_start: 0.8077 (ptt90) cc_final: 0.7652 (ptt-90) REVERT: E 66 TYR cc_start: 0.7154 (p90) cc_final: 0.6944 (p90) REVERT: E 82 THR cc_start: 0.7777 (m) cc_final: 0.7564 (p) REVERT: E 248 LEU cc_start: 0.8493 (mm) cc_final: 0.8135 (tt) REVERT: E 270 THR cc_start: 0.8468 (m) cc_final: 0.8216 (t) REVERT: E 272 ASN cc_start: 0.7965 (m-40) cc_final: 0.7747 (m110) outliers start: 39 outliers final: 25 residues processed: 234 average time/residue: 0.2184 time to fit residues: 75.0244 Evaluate side-chains 217 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 187 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain E residue 246 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN B 144 ASN B 267 ASN ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11750 Z= 0.336 Angle : 0.722 10.343 15840 Z= 0.350 Chirality : 0.046 0.157 1795 Planarity : 0.004 0.054 1980 Dihedral : 10.005 138.265 1595 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 4.24 % Allowed : 19.14 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.23), residues: 1415 helix: 1.03 (0.28), residues: 360 sheet: -0.81 (0.27), residues: 400 loop : -1.07 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 284 HIS 0.002 0.001 HIS C 265 PHE 0.016 0.002 PHE D 59 TYR 0.022 0.002 TYR A 137 ARG 0.007 0.001 ARG C 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 181 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8215 (t0) cc_final: 0.7839 (t0) REVERT: A 76 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8313 (ttmt) REVERT: A 110 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8292 (p0) REVERT: A 148 ASP cc_start: 0.7466 (p0) cc_final: 0.6999 (p0) REVERT: A 214 ASP cc_start: 0.8033 (m-30) cc_final: 0.7684 (m-30) REVERT: A 241 ILE cc_start: 0.9171 (mm) cc_final: 0.8946 (mm) REVERT: A 249 MET cc_start: 0.8465 (ttp) cc_final: 0.8100 (tmm) REVERT: B 65 ASP cc_start: 0.7700 (t0) cc_final: 0.7350 (t0) REVERT: B 95 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7316 (mp10) REVERT: B 128 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7727 (tmm) REVERT: B 169 ILE cc_start: 0.9162 (mt) cc_final: 0.8628 (tt) REVERT: C 65 ASP cc_start: 0.7441 (t70) cc_final: 0.7153 (t0) REVERT: C 95 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7899 (mt0) REVERT: C 132 GLU cc_start: 0.8339 (tp30) cc_final: 0.8072 (tp30) REVERT: C 196 ASP cc_start: 0.8044 (p0) cc_final: 0.7717 (p0) REVERT: D 40 ARG cc_start: 0.8235 (ptt-90) cc_final: 0.7743 (ptp90) REVERT: D 95 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7425 (mp10) REVERT: D 127 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8871 (pt) REVERT: D 248 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8701 (tt) REVERT: E 96 MET cc_start: 0.6169 (mmp) cc_final: 0.5392 (mmp) REVERT: E 99 LYS cc_start: 0.8358 (ptmm) cc_final: 0.7995 (tmtt) REVERT: E 214 ASP cc_start: 0.7185 (OUTLIER) cc_final: 0.6977 (m-30) REVERT: E 248 LEU cc_start: 0.8796 (mm) cc_final: 0.8377 (tt) REVERT: E 270 THR cc_start: 0.8555 (m) cc_final: 0.8285 (t) REVERT: E 272 ASN cc_start: 0.8233 (m-40) cc_final: 0.8010 (m-40) outliers start: 54 outliers final: 34 residues processed: 223 average time/residue: 0.2038 time to fit residues: 67.0797 Evaluate side-chains 214 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 171 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain E residue 246 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.9990 chunk 125 optimal weight: 20.0000 chunk 129 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11750 Z= 0.295 Angle : 0.714 12.980 15840 Z= 0.345 Chirality : 0.045 0.154 1795 Planarity : 0.004 0.053 1980 Dihedral : 9.800 136.760 1595 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 3.37 % Allowed : 20.16 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.23), residues: 1415 helix: 1.03 (0.28), residues: 360 sheet: -0.86 (0.27), residues: 400 loop : -1.08 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 284 HIS 0.004 0.001 HIS C 265 PHE 0.012 0.001 PHE A 59 TYR 0.018 0.001 TYR A 137 ARG 0.006 0.001 ARG C 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 174 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8190 (t0) cc_final: 0.7869 (t0) REVERT: A 148 ASP cc_start: 0.7475 (p0) cc_final: 0.6971 (p0) REVERT: A 214 ASP cc_start: 0.8033 (m-30) cc_final: 0.7707 (m-30) REVERT: A 232 TYR cc_start: 0.8366 (m-10) cc_final: 0.8017 (m-10) REVERT: A 241 ILE cc_start: 0.9160 (mm) cc_final: 0.8934 (mm) REVERT: A 249 MET cc_start: 0.8431 (ttp) cc_final: 0.8086 (tmm) REVERT: B 65 ASP cc_start: 0.7722 (t0) cc_final: 0.7382 (t0) REVERT: B 95 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7306 (mp10) REVERT: B 128 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7689 (tmm) REVERT: B 169 ILE cc_start: 0.9166 (mt) cc_final: 0.8607 (tt) REVERT: C 65 ASP cc_start: 0.7529 (t70) cc_final: 0.7304 (t0) REVERT: C 95 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7916 (mt0) REVERT: C 132 GLU cc_start: 0.8246 (tp30) cc_final: 0.7851 (tp30) REVERT: C 196 ASP cc_start: 0.8073 (p0) cc_final: 0.7713 (p0) REVERT: D 40 ARG cc_start: 0.8216 (ptt-90) cc_final: 0.7757 (ptp90) REVERT: D 95 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7430 (mp10) REVERT: D 127 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8689 (pt) REVERT: D 248 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8687 (tt) REVERT: E 87 LEU cc_start: 0.9249 (tp) cc_final: 0.8651 (pt) REVERT: E 96 MET cc_start: 0.6230 (mmp) cc_final: 0.5671 (mmp) REVERT: E 99 LYS cc_start: 0.8356 (ptmm) cc_final: 0.8140 (tmtt) REVERT: E 214 ASP cc_start: 0.7190 (OUTLIER) cc_final: 0.6984 (m-30) REVERT: E 248 LEU cc_start: 0.8776 (mm) cc_final: 0.8338 (tt) REVERT: E 270 THR cc_start: 0.8555 (m) cc_final: 0.8311 (t) outliers start: 43 outliers final: 30 residues processed: 208 average time/residue: 0.2105 time to fit residues: 64.7544 Evaluate side-chains 208 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 171 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain E residue 246 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 128 optimal weight: 50.0000 chunk 111 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11750 Z= 0.326 Angle : 0.742 14.867 15840 Z= 0.359 Chirality : 0.046 0.187 1795 Planarity : 0.004 0.054 1980 Dihedral : 9.817 137.385 1595 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 3.61 % Allowed : 20.63 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.23), residues: 1415 helix: 0.95 (0.28), residues: 360 sheet: -0.90 (0.27), residues: 400 loop : -1.10 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 284 HIS 0.002 0.001 HIS A 265 PHE 0.014 0.002 PHE D 59 TYR 0.021 0.001 TYR A 137 ARG 0.006 0.001 ARG C 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 165 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8142 (t0) cc_final: 0.7806 (t0) REVERT: A 148 ASP cc_start: 0.7453 (p0) cc_final: 0.6918 (p0) REVERT: A 214 ASP cc_start: 0.8067 (m-30) cc_final: 0.7746 (m-30) REVERT: A 241 ILE cc_start: 0.9152 (mm) cc_final: 0.8925 (mm) REVERT: A 249 MET cc_start: 0.8395 (ttp) cc_final: 0.8029 (tmm) REVERT: B 65 ASP cc_start: 0.7737 (t0) cc_final: 0.7382 (t0) REVERT: B 95 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7285 (mp10) REVERT: B 128 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7738 (tmm) REVERT: B 169 ILE cc_start: 0.9199 (mt) cc_final: 0.8647 (tt) REVERT: C 64 ARG cc_start: 0.7564 (ptt-90) cc_final: 0.7276 (ptt-90) REVERT: C 65 ASP cc_start: 0.7516 (t70) cc_final: 0.7269 (t0) REVERT: C 95 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7881 (mt0) REVERT: C 132 GLU cc_start: 0.8209 (tp30) cc_final: 0.7975 (tp30) REVERT: C 166 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.8080 (p0) REVERT: C 196 ASP cc_start: 0.8087 (p0) cc_final: 0.7728 (p0) REVERT: D 40 ARG cc_start: 0.8278 (ptt-90) cc_final: 0.7778 (ptp90) REVERT: D 95 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7449 (mp10) REVERT: D 127 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8824 (pt) REVERT: D 128 MET cc_start: 0.8158 (mmm) cc_final: 0.7927 (mmt) REVERT: D 248 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8740 (tt) REVERT: E 64 ARG cc_start: 0.8179 (ptt90) cc_final: 0.7918 (ptt-90) REVERT: E 87 LEU cc_start: 0.9289 (tp) cc_final: 0.8681 (pt) REVERT: E 99 LYS cc_start: 0.8369 (ptmm) cc_final: 0.8123 (tmtt) REVERT: E 214 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6943 (m-30) REVERT: E 248 LEU cc_start: 0.8905 (mm) cc_final: 0.8424 (tt) REVERT: E 270 THR cc_start: 0.8594 (m) cc_final: 0.8355 (t) outliers start: 46 outliers final: 32 residues processed: 201 average time/residue: 0.2241 time to fit residues: 67.2402 Evaluate side-chains 202 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 162 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain E residue 246 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.2980 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 97 optimal weight: 0.0770 chunk 6 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN E 10 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.124740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.099615 restraints weight = 24115.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.102833 restraints weight = 13855.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.105081 restraints weight = 9484.628| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11750 Z= 0.193 Angle : 0.672 11.402 15840 Z= 0.322 Chirality : 0.044 0.161 1795 Planarity : 0.003 0.048 1980 Dihedral : 9.229 133.864 1595 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.67 % Allowed : 21.80 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.23), residues: 1415 helix: 1.19 (0.29), residues: 360 sheet: -0.78 (0.27), residues: 400 loop : -1.03 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 284 HIS 0.002 0.001 HIS C 265 PHE 0.010 0.001 PHE C 38 TYR 0.020 0.001 TYR A 137 ARG 0.006 0.001 ARG C 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2471.62 seconds wall clock time: 46 minutes 57.72 seconds (2817.72 seconds total)