Starting phenix.real_space_refine on Fri Feb 16 12:42:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efv_28101/02_2024/8efv_28101_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efv_28101/02_2024/8efv_28101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efv_28101/02_2024/8efv_28101.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efv_28101/02_2024/8efv_28101.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efv_28101/02_2024/8efv_28101_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efv_28101/02_2024/8efv_28101_updated.pdb" } resolution = 2.97 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= 0.003 sd= 0.095 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 56 5.49 5 Mg 4 5.21 5 S 26 5.16 5 C 9531 2.51 5 N 2769 2.21 5 O 2909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15295 Number of models: 1 Model: "" Number of chains: 14 Chain: "D" Number of atoms: 2324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2324 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 277} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2355 Classifications: {'peptide': 301} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2453 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2442 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 293} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2345 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2340 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 426 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "H" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 432 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.52, per 1000 atoms: 0.56 Number of scatterers: 15295 At special positions: 0 Unit cell: (120.96, 135, 101.52, 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 26 16.00 P 56 15.00 Mg 4 11.99 O 2909 8.00 N 2769 7.00 C 9531 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: 5.94 Conformation dependent library (CDL) restraints added in 2.6 seconds 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 99 helices and 14 sheets defined 47.7% alpha, 8.0% beta 17 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 5.97 Creating SS restraints... Processing helix chain 'D' and resid 18 through 33 removed outlier: 3.714A pdb=" N LYS D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 62 Processing helix chain 'D' and resid 79 through 86 Processing helix chain 'D' and resid 99 through 101 No H-bonds generated for 'chain 'D' and resid 99 through 101' Processing helix chain 'D' and resid 104 through 109 removed outlier: 4.142A pdb=" N HIS D 109 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 115 removed outlier: 4.221A pdb=" N GLU D 115 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 153 through 157 Processing helix chain 'D' and resid 170 through 184 Processing helix chain 'D' and resid 190 through 199 removed outlier: 3.530A pdb=" N ARG D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 221 Processing helix chain 'D' and resid 228 through 237 Processing helix chain 'D' and resid 247 through 258 Processing helix chain 'D' and resid 267 through 274 Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 286 through 289 No H-bonds generated for 'chain 'D' and resid 286 through 289' Processing helix chain 'D' and resid 306 through 311 Processing helix chain 'C' and resid 18 through 33 removed outlier: 3.800A pdb=" N LYS C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 62 Processing helix chain 'C' and resid 78 through 86 removed outlier: 3.920A pdb=" N ALA C 82 " --> pdb=" O GLY C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 153 through 158 removed outlier: 3.835A pdb=" N ARG C 158 " --> pdb=" O PRO C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 184 Processing helix chain 'C' and resid 190 through 199 removed outlier: 3.533A pdb=" N GLU C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 221 Processing helix chain 'C' and resid 228 through 238 Processing helix chain 'C' and resid 247 through 258 removed outlier: 3.586A pdb=" N ILE C 252 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 273 Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 306 through 311 Processing helix chain 'B' and resid 18 through 33 removed outlier: 3.720A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 62 removed outlier: 3.511A pdb=" N HIS B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 86 removed outlier: 3.663A pdb=" N ALA B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 101 No H-bonds generated for 'chain 'B' and resid 99 through 101' Processing helix chain 'B' and resid 104 through 109 removed outlier: 3.740A pdb=" N GLU B 108 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS B 109 " --> pdb=" O GLN B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 104 through 109' Processing helix chain 'B' and resid 111 through 114 No H-bonds generated for 'chain 'B' and resid 111 through 114' Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 153 through 158 removed outlier: 3.766A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 184 Processing helix chain 'B' and resid 190 through 199 removed outlier: 3.552A pdb=" N ARG B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 221 Processing helix chain 'B' and resid 228 through 238 Processing helix chain 'B' and resid 247 through 258 Processing helix chain 'B' and resid 267 through 273 Processing helix chain 'B' and resid 278 through 284 Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'A' and resid 18 through 33 removed outlier: 3.598A pdb=" N LYS A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 62 Processing helix chain 'A' and resid 77 through 85 Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.579A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 184 Processing helix chain 'A' and resid 190 through 199 Processing helix chain 'A' and resid 204 through 220 Processing helix chain 'A' and resid 228 through 238 Processing helix chain 'A' and resid 247 through 258 Processing helix chain 'A' and resid 267 through 273 Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'F' and resid 18 through 34 removed outlier: 3.821A pdb=" N LYS F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 62 Processing helix chain 'F' and resid 80 through 85 Processing helix chain 'F' and resid 99 through 101 No H-bonds generated for 'chain 'F' and resid 99 through 101' Processing helix chain 'F' and resid 107 through 115 removed outlier: 4.000A pdb=" N TYR F 111 " --> pdb=" O GLU F 107 " (cutoff:3.500A) Proline residue: F 112 - end of helix Processing helix chain 'F' and resid 148 through 150 No H-bonds generated for 'chain 'F' and resid 148 through 150' Processing helix chain 'F' and resid 155 through 157 No H-bonds generated for 'chain 'F' and resid 155 through 157' Processing helix chain 'F' and resid 170 through 184 Processing helix chain 'F' and resid 190 through 199 Processing helix chain 'F' and resid 204 through 220 removed outlier: 3.730A pdb=" N VAL F 220 " --> pdb=" O ASP F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 238 Processing helix chain 'F' and resid 247 through 260 removed outlier: 3.871A pdb=" N ARG F 259 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 270 No H-bonds generated for 'chain 'F' and resid 267 through 270' Processing helix chain 'F' and resid 280 through 282 No H-bonds generated for 'chain 'F' and resid 280 through 282' Processing helix chain 'F' and resid 286 through 292 Processing helix chain 'F' and resid 306 through 311 Processing helix chain 'E' and resid 23 through 34 Processing helix chain 'E' and resid 51 through 62 Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 79 through 85 Processing helix chain 'E' and resid 99 through 101 No H-bonds generated for 'chain 'E' and resid 99 through 101' Processing helix chain 'E' and resid 107 through 114 removed outlier: 4.179A pdb=" N TYR E 111 " --> pdb=" O GLU E 108 " (cutoff:3.500A) Proline residue: E 112 - end of helix Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 153 through 158 removed outlier: 3.824A pdb=" N ARG E 158 " --> pdb=" O PRO E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 184 Processing helix chain 'E' and resid 190 through 199 removed outlier: 3.635A pdb=" N GLU E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 221 Processing helix chain 'E' and resid 228 through 238 Processing helix chain 'E' and resid 247 through 260 Processing helix chain 'E' and resid 269 through 273 Processing helix chain 'E' and resid 286 through 291 Processing helix chain 'E' and resid 307 through 311 Processing sheet with id= A, first strand: chain 'D' and resid 161 through 164 removed outlier: 6.327A pdb=" N ASP D 92 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ILE D 142 " --> pdb=" O ASP D 92 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU D 94 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ALA D 144 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE D 96 " --> pdb=" O ALA D 144 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 296 through 298 Processing sheet with id= C, first strand: chain 'C' and resid 161 through 164 Processing sheet with id= D, first strand: chain 'C' and resid 296 through 298 Processing sheet with id= E, first strand: chain 'B' and resid 161 through 165 removed outlier: 3.749A pdb=" N GLY B 45 " --> pdb=" O THR B 145 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 120 through 123 Processing sheet with id= G, first strand: chain 'B' and resid 295 through 298 Processing sheet with id= H, first strand: chain 'A' and resid 161 through 164 Processing sheet with id= I, first strand: chain 'A' and resid 118 through 123 Processing sheet with id= J, first strand: chain 'A' and resid 295 through 297 Processing sheet with id= K, first strand: chain 'F' and resid 161 through 164 removed outlier: 3.668A pdb=" N ALA F 144 " --> pdb=" O ILE F 96 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 295 through 297 Processing sheet with id= M, first strand: chain 'E' and resid 142 through 145 removed outlier: 6.764A pdb=" N LEU E 41 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N THR E 145 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU E 43 " --> pdb=" O THR E 145 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE E 161 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N PHE E 44 " --> pdb=" O ILE E 161 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU E 163 " --> pdb=" O PHE E 44 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 296 through 298 551 hydrogen bonds defined for protein. 1605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 4.73 Time building geometry restraints manager: 6.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 5217 1.36 - 1.51: 4047 1.51 - 1.66: 6332 1.66 - 1.80: 42 1.80 - 1.95: 7 Bond restraints: 15645 Sorted by residual: bond pdb=" CA ARG E 104 " pdb=" C ARG E 104 " ideal model delta sigma weight residual 1.522 1.546 -0.024 1.72e-02 3.38e+03 1.91e+00 bond pdb=" C3' DA G 3 " pdb=" O3' DA G 3 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.53e+00 bond pdb=" C4 ADP A 400 " pdb=" C5 ADP A 400 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.22e+00 bond pdb=" C4 ADP E 400 " pdb=" C5 ADP E 400 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.05e+00 bond pdb=" C4 ADP F 400 " pdb=" C5 ADP F 400 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.01e+00 ... (remaining 15640 not shown) Histogram of bond angle deviations from ideal: 99.85 - 107.07: 843 107.07 - 114.29: 9147 114.29 - 121.51: 7726 121.51 - 128.72: 3553 128.72 - 135.94: 105 Bond angle restraints: 21374 Sorted by residual: angle pdb=" N GLY A 16 " pdb=" CA GLY A 16 " pdb=" C GLY A 16 " ideal model delta sigma weight residual 113.18 120.68 -7.50 2.37e+00 1.78e-01 1.00e+01 angle pdb=" N GLY C 16 " pdb=" CA GLY C 16 " pdb=" C GLY C 16 " ideal model delta sigma weight residual 113.18 120.43 -7.25 2.37e+00 1.78e-01 9.36e+00 angle pdb=" N GLY D 16 " pdb=" CA GLY D 16 " pdb=" C GLY D 16 " ideal model delta sigma weight residual 113.18 120.02 -6.84 2.37e+00 1.78e-01 8.32e+00 angle pdb=" N GLY F 16 " pdb=" CA GLY F 16 " pdb=" C GLY F 16 " ideal model delta sigma weight residual 113.18 119.61 -6.43 2.37e+00 1.78e-01 7.37e+00 angle pdb=" N GLY B 16 " pdb=" CA GLY B 16 " pdb=" C GLY B 16 " ideal model delta sigma weight residual 113.18 119.59 -6.41 2.37e+00 1.78e-01 7.32e+00 ... (remaining 21369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.01: 9086 34.01 - 68.03: 357 68.03 - 102.04: 19 102.04 - 136.05: 5 136.05 - 170.07: 2 Dihedral angle restraints: 9469 sinusoidal: 4295 harmonic: 5174 Sorted by residual: dihedral pdb=" O2A ADP A 400 " pdb=" O3A ADP A 400 " pdb=" PA ADP A 400 " pdb=" PB ADP A 400 " ideal model delta sinusoidal sigma weight residual 300.00 167.74 132.26 1 2.00e+01 2.50e-03 4.01e+01 dihedral pdb=" O1B ADP E 400 " pdb=" O3A ADP E 400 " pdb=" PB ADP E 400 " pdb=" PA ADP E 400 " ideal model delta sinusoidal sigma weight residual 300.00 178.00 122.00 1 2.00e+01 2.50e-03 3.67e+01 dihedral pdb=" O1B ADP F 400 " pdb=" O3A ADP F 400 " pdb=" PB ADP F 400 " pdb=" PA ADP F 400 " ideal model delta sinusoidal sigma weight residual -60.00 61.76 -121.77 1 2.00e+01 2.50e-03 3.66e+01 ... (remaining 9466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1625 0.030 - 0.060: 549 0.060 - 0.090: 152 0.090 - 0.121: 126 0.121 - 0.151: 5 Chirality restraints: 2457 Sorted by residual: chirality pdb=" CA ILE D 290 " pdb=" N ILE D 290 " pdb=" C ILE D 290 " pdb=" CB ILE D 290 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA ILE B 151 " pdb=" N ILE B 151 " pdb=" C ILE B 151 " pdb=" CB ILE B 151 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" P DT G 4 " pdb=" OP1 DT G 4 " pdb=" OP2 DT G 4 " pdb=" O5' DT G 4 " both_signs ideal model delta sigma weight residual True 2.35 -2.47 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 2454 not shown) Planarity restraints: 2607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 298 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO D 299 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 299 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 299 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 169 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.47e+00 pdb=" N PRO F 170 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO F 170 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 170 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 169 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO C 170 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 170 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 170 " -0.026 5.00e-02 4.00e+02 ... (remaining 2604 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 119 2.59 - 3.17: 11780 3.17 - 3.75: 23533 3.75 - 4.32: 33270 4.32 - 4.90: 55380 Nonbonded interactions: 124082 Sorted by model distance: nonbonded pdb=" OD1 ASP A 97 " pdb="MG MG A 401 " model vdw 2.016 2.170 nonbonded pdb=" OG1 THR F 52 " pdb=" O2B ADP F 400 " model vdw 2.177 2.440 nonbonded pdb=" O GLY D 293 " pdb=" OG1 THR D 305 " model vdw 2.191 2.440 nonbonded pdb=" ND1 HIS B 100 " pdb=" OG1 THR B 145 " model vdw 2.276 2.520 nonbonded pdb=" O LEU D 49 " pdb=" OH TYR D 168 " model vdw 2.280 2.440 ... (remaining 124077 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' and (resid 7 through 74 or resid 77 through 118 or (resid 119 and (na \ me N or name CA or name C or name O or name CB )) or resid 133 through 137 or (r \ esid 138 and (name N or name CA or name C or name O )) or resid 139 through 317) \ ) selection = (chain 'B' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 137 or (resid 138 and (name N or \ name CA or name C or name O )) or resid 139 through 317)) selection = (chain 'C' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 317)) selection = (chain 'D' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 137 or (resid 138 and (name N or \ name CA or name C or name O )) or resid 139 through 317)) selection = (chain 'E' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 137 or (resid 138 and (name N or \ name CA or name C or name O )) or resid 139 through 317)) selection = (chain 'F' and (resid 7 through 119 or resid 133 through 137 or (resid 138 and ( \ name N or name CA or name C or name O )) or resid 139 through 317)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 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: 3.130 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 44.400 Find NCS groups from input model: 1.220 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:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 0.037 15645 Z= 0.184 Angle : 0.576 7.501 21374 Z= 0.280 Chirality : 0.039 0.151 2457 Planarity : 0.005 0.047 2607 Dihedral : 17.042 170.067 6149 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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 (0.20), residues: 1791 helix: 1.00 (0.17), residues: 955 sheet: 0.26 (0.37), residues: 216 loop : -0.01 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 40 PHE 0.010 0.001 PHE A 211 TYR 0.008 0.001 TYR C 111 ARG 0.003 0.000 ARG E 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.627 Fit side-chains REVERT: C 216 ASP cc_start: 0.8420 (m-30) cc_final: 0.8145 (m-30) REVERT: B 65 ASN cc_start: 0.8098 (m110) cc_final: 0.7794 (m-40) REVERT: B 191 GLU cc_start: 0.7989 (mp0) cc_final: 0.7777 (mp0) REVERT: B 310 ARG cc_start: 0.8173 (mtm-85) cc_final: 0.7966 (mtm-85) REVERT: A 204 MET cc_start: 0.8848 (tpp) cc_final: 0.8181 (tpt) REVERT: F 243 LEU cc_start: 0.7966 (mt) cc_final: 0.7757 (mt) REVERT: E 198 ARG cc_start: 0.7487 (mtt-85) cc_final: 0.7257 (mtt-85) outliers start: 0 outliers final: 1 residues processed: 220 average time/residue: 1.8338 time to fit residues: 432.1824 Evaluate side-chains 183 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 183 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 chunk 143 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.0604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15645 Z= 0.202 Angle : 0.579 8.258 21374 Z= 0.276 Chirality : 0.039 0.155 2457 Planarity : 0.005 0.055 2607 Dihedral : 17.017 170.868 2593 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.61 % Allowed : 8.29 % Favored : 91.09 % 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: 0.80 (0.20), residues: 1791 helix: 1.04 (0.17), residues: 954 sheet: 0.21 (0.36), residues: 229 loop : 0.04 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 40 PHE 0.012 0.001 PHE A 44 TYR 0.009 0.001 TYR C 111 ARG 0.008 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 187 time to evaluate : 1.868 Fit side-chains REVERT: C 216 ASP cc_start: 0.8465 (m-30) cc_final: 0.8151 (m-30) REVERT: A 204 MET cc_start: 0.8856 (tpp) cc_final: 0.8226 (tpt) REVERT: F 243 LEU cc_start: 0.7960 (mt) cc_final: 0.7735 (mt) REVERT: E 190 GLU cc_start: 0.7227 (pm20) cc_final: 0.6588 (tp30) REVERT: E 198 ARG cc_start: 0.7514 (mtt-85) cc_final: 0.7259 (mtt-85) outliers start: 9 outliers final: 5 residues processed: 191 average time/residue: 1.8111 time to fit residues: 371.9087 Evaluate side-chains 175 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 170 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 242 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 138 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 166 optimal weight: 0.4980 chunk 179 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15645 Z= 0.196 Angle : 0.567 9.589 21374 Z= 0.269 Chirality : 0.038 0.153 2457 Planarity : 0.005 0.058 2607 Dihedral : 16.859 170.806 2593 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.16 % Allowed : 10.67 % Favored : 88.17 % 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: 0.81 (0.20), residues: 1791 helix: 1.09 (0.17), residues: 953 sheet: 0.12 (0.35), residues: 234 loop : 0.01 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 100 PHE 0.011 0.001 PHE A 44 TYR 0.009 0.001 TYR C 111 ARG 0.009 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 181 time to evaluate : 1.828 Fit side-chains REVERT: C 216 ASP cc_start: 0.8399 (m-30) cc_final: 0.8122 (m-30) REVERT: C 283 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: B 32 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7861 (mtmp) REVERT: A 9 LYS cc_start: 0.8265 (ptpp) cc_final: 0.7932 (ptpt) REVERT: A 89 GLU cc_start: 0.7693 (tt0) cc_final: 0.7473 (tt0) REVERT: A 204 MET cc_start: 0.8867 (tpp) cc_final: 0.8244 (tpt) REVERT: F 243 LEU cc_start: 0.7892 (mt) cc_final: 0.7638 (mt) REVERT: E 119 MET cc_start: 0.6787 (OUTLIER) cc_final: 0.6416 (ttt) REVERT: E 198 ARG cc_start: 0.7494 (mtt-85) cc_final: 0.7229 (mtt-85) outliers start: 17 outliers final: 5 residues processed: 191 average time/residue: 1.7929 time to fit residues: 367.8795 Evaluate side-chains 176 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain E residue 119 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 164 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 111 optimal weight: 0.3980 chunk 167 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN E 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15645 Z= 0.159 Angle : 0.545 9.922 21374 Z= 0.259 Chirality : 0.038 0.147 2457 Planarity : 0.005 0.061 2607 Dihedral : 16.545 170.305 2593 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.09 % Allowed : 13.12 % Favored : 85.79 % 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: 0.96 (0.20), residues: 1791 helix: 1.25 (0.17), residues: 952 sheet: 0.01 (0.35), residues: 232 loop : 0.09 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 40 PHE 0.010 0.001 PHE A 44 TYR 0.008 0.001 TYR C 111 ARG 0.010 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 184 time to evaluate : 1.802 Fit side-chains REVERT: C 216 ASP cc_start: 0.8284 (m-30) cc_final: 0.8041 (m-30) REVERT: C 283 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: C 296 LYS cc_start: 0.8343 (mtmt) cc_final: 0.8064 (ttmt) REVERT: B 32 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7837 (mtmp) REVERT: A 9 LYS cc_start: 0.8259 (ptpp) cc_final: 0.7930 (ptpt) REVERT: A 89 GLU cc_start: 0.7692 (tt0) cc_final: 0.7472 (tt0) REVERT: A 204 MET cc_start: 0.8829 (tpp) cc_final: 0.8164 (tpt) REVERT: F 243 LEU cc_start: 0.7892 (mt) cc_final: 0.7638 (mt) REVERT: E 36 GLU cc_start: 0.7849 (pm20) cc_final: 0.7482 (pm20) REVERT: E 190 GLU cc_start: 0.7207 (pm20) cc_final: 0.6527 (tp30) outliers start: 16 outliers final: 7 residues processed: 192 average time/residue: 1.7223 time to fit residues: 356.1722 Evaluate side-chains 181 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 172 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain E residue 116 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 147 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 150 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15645 Z= 0.227 Angle : 0.582 11.824 21374 Z= 0.274 Chirality : 0.039 0.215 2457 Planarity : 0.005 0.061 2607 Dihedral : 16.569 171.527 2593 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.50 % Allowed : 13.66 % Favored : 84.84 % 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: 0.85 (0.20), residues: 1791 helix: 1.14 (0.17), residues: 957 sheet: 0.01 (0.34), residues: 232 loop : 0.05 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 40 PHE 0.012 0.001 PHE A 44 TYR 0.011 0.001 TYR C 111 ARG 0.012 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 181 time to evaluate : 1.758 Fit side-chains REVERT: C 166 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7367 (mt-10) REVERT: C 216 ASP cc_start: 0.8403 (m-30) cc_final: 0.8137 (m-30) REVERT: C 283 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: B 32 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7867 (mtmp) REVERT: A 9 LYS cc_start: 0.8266 (ptpp) cc_final: 0.8064 (ptpt) REVERT: A 89 GLU cc_start: 0.7700 (tt0) cc_final: 0.7477 (tt0) REVERT: A 204 MET cc_start: 0.8896 (tpp) cc_final: 0.8218 (tpt) REVERT: F 190 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6430 (pm20) REVERT: F 243 LEU cc_start: 0.7905 (mt) cc_final: 0.7661 (mt) REVERT: E 119 MET cc_start: 0.6833 (OUTLIER) cc_final: 0.6452 (ttt) outliers start: 22 outliers final: 9 residues processed: 192 average time/residue: 1.8503 time to fit residues: 381.5907 Evaluate side-chains 182 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 168 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 296 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 119 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 59 optimal weight: 0.1980 chunk 159 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 0.0050 chunk 43 optimal weight: 0.5980 chunk 177 optimal weight: 1.9990 chunk 146 optimal weight: 30.0000 chunk 81 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15645 Z= 0.162 Angle : 0.548 8.745 21374 Z= 0.261 Chirality : 0.038 0.145 2457 Planarity : 0.005 0.060 2607 Dihedral : 16.423 170.268 2591 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.36 % Allowed : 14.62 % Favored : 84.02 % 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: 0.98 (0.20), residues: 1791 helix: 1.26 (0.17), residues: 957 sheet: 0.02 (0.34), residues: 232 loop : 0.11 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 40 PHE 0.010 0.001 PHE A 44 TYR 0.008 0.001 TYR C 111 ARG 0.009 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 175 time to evaluate : 1.761 Fit side-chains REVERT: C 216 ASP cc_start: 0.8301 (m-30) cc_final: 0.8042 (m-30) REVERT: C 283 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.8033 (mt-10) REVERT: C 296 LYS cc_start: 0.8344 (mtmt) cc_final: 0.8074 (ttmt) REVERT: B 32 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7832 (mtmp) REVERT: B 191 GLU cc_start: 0.7933 (mp0) cc_final: 0.7717 (mp0) REVERT: A 9 LYS cc_start: 0.8253 (ptpp) cc_final: 0.8044 (ptpt) REVERT: A 89 GLU cc_start: 0.7687 (tt0) cc_final: 0.7467 (tt0) REVERT: A 204 MET cc_start: 0.8851 (tpp) cc_final: 0.8206 (tpt) REVERT: F 243 LEU cc_start: 0.7928 (mt) cc_final: 0.7688 (mt) outliers start: 20 outliers final: 8 residues processed: 190 average time/residue: 1.6629 time to fit residues: 341.3224 Evaluate side-chains 177 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 167 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain E residue 116 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 170 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 98 optimal weight: 0.0270 chunk 176 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 109 HIS F 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15645 Z= 0.198 Angle : 0.569 9.954 21374 Z= 0.269 Chirality : 0.038 0.152 2457 Planarity : 0.005 0.060 2607 Dihedral : 16.450 171.197 2591 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.56 % Allowed : 14.75 % Favored : 83.68 % 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: 0.92 (0.20), residues: 1791 helix: 1.20 (0.17), residues: 956 sheet: 0.05 (0.34), residues: 232 loop : 0.07 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 40 PHE 0.011 0.001 PHE A 44 TYR 0.009 0.001 TYR C 111 ARG 0.010 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 169 time to evaluate : 1.663 Fit side-chains REVERT: C 166 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7359 (mt-10) REVERT: C 216 ASP cc_start: 0.8355 (m-30) cc_final: 0.8108 (m-30) REVERT: C 283 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: B 32 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7851 (mtmp) REVERT: B 92 ASP cc_start: 0.8321 (p0) cc_final: 0.7987 (m-30) REVERT: B 191 GLU cc_start: 0.7942 (mp0) cc_final: 0.7714 (mp0) REVERT: A 9 LYS cc_start: 0.8288 (ptpp) cc_final: 0.8076 (ptpt) REVERT: A 89 GLU cc_start: 0.7702 (tt0) cc_final: 0.7486 (tt0) REVERT: A 204 MET cc_start: 0.8886 (tpp) cc_final: 0.8231 (tpt) REVERT: A 283 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: F 243 LEU cc_start: 0.7934 (mt) cc_final: 0.7688 (mt) REVERT: E 119 MET cc_start: 0.6863 (OUTLIER) cc_final: 0.6496 (ttt) outliers start: 23 outliers final: 11 residues processed: 183 average time/residue: 1.7138 time to fit residues: 337.8740 Evaluate side-chains 181 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 119 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 87 optimal weight: 0.0980 chunk 16 optimal weight: 0.3980 chunk 138 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15645 Z= 0.152 Angle : 0.541 12.372 21374 Z= 0.257 Chirality : 0.037 0.143 2457 Planarity : 0.005 0.060 2607 Dihedral : 16.277 169.817 2591 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.50 % Allowed : 15.02 % Favored : 83.48 % 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: 1.10 (0.21), residues: 1791 helix: 1.33 (0.17), residues: 957 sheet: 0.11 (0.35), residues: 229 loop : 0.19 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 40 PHE 0.010 0.001 PHE A 44 TYR 0.007 0.001 TYR C 111 ARG 0.009 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 175 time to evaluate : 1.624 Fit side-chains REVERT: C 216 ASP cc_start: 0.8235 (m-30) cc_final: 0.8024 (m-30) REVERT: C 283 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.8011 (mt-10) REVERT: C 296 LYS cc_start: 0.8334 (mtmt) cc_final: 0.8058 (ttmt) REVERT: B 32 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7824 (mtmp) REVERT: B 191 GLU cc_start: 0.7939 (mp0) cc_final: 0.7709 (mp0) REVERT: B 259 ARG cc_start: 0.7686 (ttt90) cc_final: 0.7293 (ttt-90) REVERT: A 9 LYS cc_start: 0.8250 (ptpp) cc_final: 0.8031 (ptpt) REVERT: A 89 GLU cc_start: 0.7693 (tt0) cc_final: 0.7480 (tt0) REVERT: A 204 MET cc_start: 0.8824 (tpp) cc_final: 0.8207 (tpt) REVERT: A 283 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: F 178 MET cc_start: 0.7746 (mtp) cc_final: 0.7453 (mmm) REVERT: F 199 ARG cc_start: 0.8507 (mpt90) cc_final: 0.8266 (mmt-90) REVERT: F 243 LEU cc_start: 0.7941 (mt) cc_final: 0.7697 (mt) REVERT: E 36 GLU cc_start: 0.7916 (pm20) cc_final: 0.7533 (pm20) outliers start: 22 outliers final: 9 residues processed: 191 average time/residue: 1.6957 time to fit residues: 350.6939 Evaluate side-chains 177 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 165 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain E residue 116 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 148 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15645 Z= 0.179 Angle : 0.562 12.338 21374 Z= 0.265 Chirality : 0.038 0.150 2457 Planarity : 0.005 0.060 2607 Dihedral : 16.316 171.108 2591 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.22 % Allowed : 15.43 % Favored : 83.34 % 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: 1.05 (0.20), residues: 1791 helix: 1.30 (0.17), residues: 958 sheet: 0.10 (0.35), residues: 229 loop : 0.15 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 40 PHE 0.010 0.001 PHE A 44 TYR 0.008 0.001 TYR C 111 ARG 0.012 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 173 time to evaluate : 1.511 Fit side-chains REVERT: C 216 ASP cc_start: 0.8278 (m-30) cc_final: 0.8040 (m-30) REVERT: C 283 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: C 296 LYS cc_start: 0.8343 (mtmt) cc_final: 0.8067 (ttmt) REVERT: B 32 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.7830 (mtmp) REVERT: B 191 GLU cc_start: 0.7945 (mp0) cc_final: 0.7709 (mp0) REVERT: B 259 ARG cc_start: 0.7682 (ttt90) cc_final: 0.7290 (ttt-90) REVERT: A 9 LYS cc_start: 0.8271 (ptpp) cc_final: 0.8046 (ptpt) REVERT: A 89 GLU cc_start: 0.7694 (tt0) cc_final: 0.7482 (tt0) REVERT: A 204 MET cc_start: 0.8865 (tpp) cc_final: 0.8231 (tpt) REVERT: A 283 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: F 178 MET cc_start: 0.7759 (mtp) cc_final: 0.7466 (mmm) REVERT: F 199 ARG cc_start: 0.8484 (mpt90) cc_final: 0.8056 (mmt-90) REVERT: F 243 LEU cc_start: 0.7907 (mt) cc_final: 0.7649 (mt) REVERT: E 36 GLU cc_start: 0.7875 (pm20) cc_final: 0.7657 (pm20) outliers start: 18 outliers final: 12 residues processed: 186 average time/residue: 1.7133 time to fit residues: 343.7871 Evaluate side-chains 187 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 172 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 173 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 145 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 112 optimal weight: 0.0040 chunk 89 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 overall best weight: 1.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15645 Z= 0.250 Angle : 0.605 12.026 21374 Z= 0.285 Chirality : 0.040 0.156 2457 Planarity : 0.005 0.059 2607 Dihedral : 16.528 171.292 2591 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.36 % Allowed : 15.70 % Favored : 82.94 % 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: 0.86 (0.20), residues: 1791 helix: 1.15 (0.17), residues: 956 sheet: 0.08 (0.35), residues: 229 loop : 0.02 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 40 PHE 0.013 0.001 PHE A 44 TYR 0.011 0.001 TYR C 111 ARG 0.010 0.000 ARG A 228 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 1.782 Fit side-chains REVERT: C 216 ASP cc_start: 0.8425 (m-30) cc_final: 0.8160 (m-30) REVERT: C 283 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8035 (mt-10) REVERT: B 32 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7854 (mtmp) REVERT: A 9 LYS cc_start: 0.8231 (ptpp) cc_final: 0.8019 (ptpt) REVERT: A 89 GLU cc_start: 0.7708 (tt0) cc_final: 0.7495 (tt0) REVERT: A 182 ARG cc_start: 0.8010 (ttp-110) cc_final: 0.7807 (ttp-110) REVERT: A 204 MET cc_start: 0.8929 (tpp) cc_final: 0.8263 (tpt) REVERT: A 283 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: F 178 MET cc_start: 0.7772 (mtp) cc_final: 0.7466 (mmm) REVERT: F 243 LEU cc_start: 0.7911 (mt) cc_final: 0.7645 (mt) outliers start: 20 outliers final: 11 residues processed: 187 average time/residue: 1.6498 time to fit residues: 333.4872 Evaluate side-chains 185 residues out of total 1480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 0.0670 chunk 145 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 149 optimal weight: 40.0000 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 0.0170 chunk 127 optimal weight: 8.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.184555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.144382 restraints weight = 15510.069| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.48 r_work: 0.3244 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15645 Z= 0.182 Angle : 0.568 12.640 21374 Z= 0.269 Chirality : 0.038 0.148 2457 Planarity : 0.005 0.060 2607 Dihedral : 16.429 169.943 2591 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.16 % Allowed : 15.91 % Favored : 82.94 % 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: 0.95 (0.20), residues: 1791 helix: 1.20 (0.17), residues: 960 sheet: 0.11 (0.35), residues: 231 loop : 0.10 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 40 PHE 0.010 0.001 PHE A 44 TYR 0.009 0.001 TYR C 111 ARG 0.012 0.000 ARG A 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5861.71 seconds wall clock time: 104 minutes 12.93 seconds (6252.93 seconds total)