Starting phenix.real_space_refine on Sat Dec 9 16:04:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x54_33007/12_2023/7x54_33007_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x54_33007/12_2023/7x54_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_33007/12_2023/7x54_33007.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x54_33007/12_2023/7x54_33007.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x54_33007/12_2023/7x54_33007_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x54_33007/12_2023/7x54_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-1.21rc1-5172/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: 6.36, per 1000 atoms: 0.55 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: 4.39 Conformation dependent library (CDL) restraints added in 2.1 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: 2.34 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: 3.28 Time building geometry restraints manager: 4.78 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: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.810 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 33.190 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.110 ------------------------------------------------------------------------------- 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 : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 322 average time/residue: 0.2625 time to fit residues: 116.1590 Evaluate side-chains 172 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 170 time to evaluate : 1.347 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1319 time to fit residues: 2.2384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0030 chunk 127 optimal weight: 4.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- 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 E 60 ASN E 69 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11750 Z= 0.406 Angle : 0.759 6.963 15840 Z= 0.385 Chirality : 0.049 0.170 1795 Planarity : 0.004 0.051 1980 Dihedral : 13.727 171.532 1595 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.43 % Allowed : 12.16 % Favored : 85.41 % 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: -1.19 (0.23), residues: 1415 helix: -0.04 (0.27), residues: 365 sheet: -0.92 (0.29), residues: 370 loop : -1.03 (0.26), residues: 680 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 0.027 0.002 PHE D 59 TYR 0.018 0.002 TYR D 253 ARG 0.006 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 228 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 197 time to evaluate : 1.387 Fit side-chains outliers start: 31 outliers final: 23 residues processed: 221 average time/residue: 0.2409 time to fit residues: 75.8401 Evaluate side-chains 171 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 1.199 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1043 time to fit residues: 6.3518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 105 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 126 optimal weight: 50.0000 chunk 43 optimal weight: 0.2980 chunk 102 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 69 GLN C 234 ASN E 60 ASN E 272 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11750 Z= 0.216 Angle : 0.638 6.711 15840 Z= 0.317 Chirality : 0.045 0.156 1795 Planarity : 0.003 0.043 1980 Dihedral : 12.284 175.672 1595 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.96 % Allowed : 14.04 % Favored : 84.00 % 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: -0.76 (0.24), residues: 1415 helix: 0.62 (0.28), residues: 365 sheet: -0.62 (0.29), residues: 370 loop : -1.00 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 284 HIS 0.002 0.001 HIS E 265 PHE 0.008 0.001 PHE C 59 TYR 0.020 0.001 TYR A 72 ARG 0.005 0.000 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 231 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 206 time to evaluate : 1.330 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 225 average time/residue: 0.2217 time to fit residues: 72.8109 Evaluate side-chains 179 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 164 time to evaluate : 1.383 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1373 time to fit residues: 5.2922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 135 optimal weight: 50.0000 chunk 121 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 267 ASN B 267 ASN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN C 267 ASN D 267 ASN E 60 ASN E 86 ASN E 267 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.110 11750 Z= 0.666 Angle : 0.928 8.598 15840 Z= 0.468 Chirality : 0.052 0.172 1795 Planarity : 0.005 0.066 1980 Dihedral : 11.623 123.227 1595 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.68 % Favored : 90.25 % Rotamer: Outliers : 5.41 % Allowed : 15.69 % Favored : 78.90 % 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: 0.08 (0.26), residues: 360 sheet: -0.72 (0.29), residues: 365 loop : -1.37 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 284 HIS 0.003 0.001 HIS C 265 PHE 0.035 0.003 PHE E 59 TYR 0.018 0.002 TYR C 218 ARG 0.008 0.001 ARG D 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 232 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 163 time to evaluate : 1.332 Fit side-chains revert: symmetry clash outliers start: 69 outliers final: 37 residues processed: 221 average time/residue: 0.2333 time to fit residues: 74.6474 Evaluate side-chains 176 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 139 time to evaluate : 1.426 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1211 time to fit residues: 9.9427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 100 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 34 optimal weight: 0.0570 chunk 45 optimal weight: 0.8980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN B 191 ASN ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN C 144 ASN D 69 GLN E 60 ASN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4960 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= 0.203 Angle : 0.666 9.421 15840 Z= 0.330 Chirality : 0.046 0.162 1795 Planarity : 0.004 0.058 1980 Dihedral : 10.849 124.283 1595 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 0.71 % Allowed : 19.92 % Favored : 79.37 % 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: -0.70 (0.23), residues: 1415 helix: 0.82 (0.28), residues: 360 sheet: -0.50 (0.29), residues: 365 loop : -1.11 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 284 HIS 0.001 0.000 HIS D 265 PHE 0.009 0.001 PHE E 23 TYR 0.013 0.001 TYR B 232 ARG 0.005 0.001 ARG D 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 220 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 211 time to evaluate : 1.387 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 218 average time/residue: 0.2280 time to fit residues: 72.7926 Evaluate side-chains 164 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 161 time to evaluate : 1.371 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1066 time to fit residues: 2.4358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.0270 chunk 26 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 135 optimal weight: 50.0000 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 0.0980 chunk 11 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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** D 69 GLN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11750 Z= 0.192 Angle : 0.657 8.391 15840 Z= 0.321 Chirality : 0.045 0.181 1795 Planarity : 0.003 0.055 1980 Dihedral : 10.405 128.547 1595 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 1.10 % Allowed : 21.96 % 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: -0.49 (0.23), residues: 1415 helix: 1.07 (0.29), residues: 360 sheet: -0.39 (0.28), residues: 365 loop : -1.00 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 284 HIS 0.001 0.001 HIS C 265 PHE 0.010 0.001 PHE C 23 TYR 0.021 0.001 TYR A 72 ARG 0.007 0.001 ARG B 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 202 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 188 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 197 average time/residue: 0.2148 time to fit residues: 62.6496 Evaluate side-chains 179 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 170 time to evaluate : 1.287 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1122 time to fit residues: 3.7660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 0.0980 chunk 114 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 0.0980 chunk 62 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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** D 69 GLN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11750 Z= 0.183 Angle : 0.662 9.417 15840 Z= 0.323 Chirality : 0.045 0.171 1795 Planarity : 0.003 0.058 1980 Dihedral : 9.979 136.636 1595 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.94 % Allowed : 23.22 % Favored : 75.84 % 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: -0.48 (0.23), residues: 1415 helix: 1.15 (0.29), residues: 360 sheet: -0.45 (0.28), residues: 370 loop : -1.00 (0.24), residues: 685 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 0.010 0.001 PHE C 23 TYR 0.014 0.001 TYR A 15 ARG 0.008 0.001 ARG E 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 197 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 185 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 195 average time/residue: 0.2168 time to fit residues: 62.3259 Evaluate side-chains 180 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 175 time to evaluate : 1.609 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1062 time to fit residues: 3.4837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7577 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11750 Z= 0.320 Angle : 0.724 10.491 15840 Z= 0.357 Chirality : 0.046 0.193 1795 Planarity : 0.004 0.060 1980 Dihedral : 10.099 134.708 1595 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 1.65 % Allowed : 22.51 % Favored : 75.84 % 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: -0.67 (0.23), residues: 1415 helix: 0.93 (0.28), residues: 360 sheet: -0.59 (0.28), residues: 380 loop : -1.06 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 284 HIS 0.002 0.001 HIS C 265 PHE 0.016 0.002 PHE D 59 TYR 0.012 0.001 TYR A 15 ARG 0.008 0.001 ARG E 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 184 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 163 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 176 average time/residue: 0.2019 time to fit residues: 53.9448 Evaluate side-chains 169 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 158 time to evaluate : 1.350 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1062 time to fit residues: 4.0367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 129 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 0.0470 chunk 38 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 82 optimal weight: 0.4980 chunk 132 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 166 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11750 Z= 0.207 Angle : 0.687 9.757 15840 Z= 0.336 Chirality : 0.045 0.183 1795 Planarity : 0.004 0.061 1980 Dihedral : 9.730 133.766 1595 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 0.47 % Allowed : 23.61 % Favored : 75.92 % 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: -0.66 (0.23), residues: 1415 helix: 1.07 (0.28), residues: 365 sheet: -0.71 (0.27), residues: 405 loop : -1.07 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 284 HIS 0.002 0.001 HIS D 265 PHE 0.009 0.001 PHE C 23 TYR 0.014 0.001 TYR A 15 ARG 0.009 0.001 ARG E 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 187 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 181 time to evaluate : 1.276 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 184 average time/residue: 0.2118 time to fit residues: 58.6993 Evaluate side-chains 166 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 1.946 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1407 time to fit residues: 3.3287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 139 optimal weight: 0.0970 chunk 128 optimal weight: 50.0000 chunk 111 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 0.0670 overall best weight: 0.7720 ------------------------------------------------------------------------------- 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** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11750 Z= 0.237 Angle : 0.702 12.277 15840 Z= 0.343 Chirality : 0.045 0.183 1795 Planarity : 0.004 0.061 1980 Dihedral : 9.477 136.779 1595 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.47 % Allowed : 23.29 % Favored : 76.24 % 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: -0.66 (0.23), residues: 1415 helix: 1.06 (0.28), residues: 365 sheet: -0.73 (0.27), residues: 405 loop : -1.05 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 284 HIS 0.001 0.001 HIS C 265 PHE 0.010 0.001 PHE A 23 TYR 0.018 0.001 TYR A 15 ARG 0.009 0.001 ARG E 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 175 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 169 time to evaluate : 1.322 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 172 average time/residue: 0.1979 time to fit residues: 51.9267 Evaluate side-chains 168 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 164 time to evaluate : 1.317 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1002 time to fit residues: 2.5996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 chunk 111 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.124663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.099941 restraints weight = 23917.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.103175 restraints weight = 13795.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.105406 restraints weight = 9342.346| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5631 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= 0.204 Angle : 0.683 9.141 15840 Z= 0.332 Chirality : 0.044 0.162 1795 Planarity : 0.004 0.060 1980 Dihedral : 9.180 135.254 1595 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.16 % Allowed : 23.76 % Favored : 76.08 % 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: -0.64 (0.23), residues: 1415 helix: 1.05 (0.28), residues: 365 sheet: -0.69 (0.27), residues: 405 loop : -1.03 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 284 HIS 0.002 0.001 HIS C 265 PHE 0.010 0.001 PHE A 23 TYR 0.021 0.001 TYR A 72 ARG 0.009 0.001 ARG E 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2453.73 seconds wall clock time: 46 minutes 11.78 seconds (2771.78 seconds total)