Starting phenix.real_space_refine on Mon Mar 11 12:40:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzs_27807/03_2024/8dzs_27807_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzs_27807/03_2024/8dzs_27807.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzs_27807/03_2024/8dzs_27807_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzs_27807/03_2024/8dzs_27807_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzs_27807/03_2024/8dzs_27807_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzs_27807/03_2024/8dzs_27807.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzs_27807/03_2024/8dzs_27807.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzs_27807/03_2024/8dzs_27807_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzs_27807/03_2024/8dzs_27807_updated.pdb" } resolution = 2.65 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= 0.001 sd= 0.023 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: 5 Type Number sf(0) Gaussians S 53 5.16 5 Cl 2 4.86 5 C 5283 2.51 5 N 1381 2.21 5 O 1526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 138": "OD1" <-> "OD2" Residue "A PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 312": "OD1" <-> "OD2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 48": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8245 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2047 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 8, 'TRANS': 261} Chain breaks: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1641 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 1, 'TRANS': 209} Chain breaks: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2482 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 8, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 94 Chain: "D" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 336 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1712 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'U9I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.02, per 1000 atoms: 0.61 Number of scatterers: 8245 At special positions: 0 Unit cell: (90.64, 118.8, 127.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 53 16.00 O 1526 8.00 N 1381 7.00 C 5283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 210 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 3.10 Conformation dependent library (CDL) restraints added in 1.7 seconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2062 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 13 sheets defined 32.3% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 61 through 86 removed outlier: 3.545A pdb=" N VAL A 65 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL A 68 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL A 69 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL A 71 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL A 72 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU A 79 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N MET A 81 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE A 82 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG A 86 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 111 removed outlier: 4.216A pdb=" N THR A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 120 removed outlier: 4.282A pdb=" N VAL A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 161 Processing helix chain 'A' and resid 165 through 169 removed outlier: 3.985A pdb=" N PHE A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 195 removed outlier: 3.678A pdb=" N SER A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'A' and resid 236 through 255 removed outlier: 4.374A pdb=" N SER A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 299 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 307 through 331 removed outlier: 3.756A pdb=" N SER A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing helix chain 'B' and resid 7 through 31 removed outlier: 3.596A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 53 removed outlier: 3.744A pdb=" N MET B 53 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 213 through 216 Processing helix chain 'B' and resid 243 through 255 Processing helix chain 'B' and resid 272 through 278 removed outlier: 4.053A pdb=" N ALA B 276 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 331 through 351 removed outlier: 3.986A pdb=" N LYS B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 24 removed outlier: 3.596A pdb=" N GLN C 9 " --> pdb=" O ASP C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 36 removed outlier: 5.128A pdb=" N ASN C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 21 removed outlier: 3.655A pdb=" N LEU D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 199 through 202 removed outlier: 4.268A pdb=" N VAL A 207 " --> pdb=" O ARG A 202 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 320 through 324 removed outlier: 6.789A pdb=" N LEU B 265 " --> pdb=" O TYR B 321 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N HIS B 323 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU B 267 " --> pdb=" O HIS B 323 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 221 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 37 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR B 196 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU B 36 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS B 198 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU B 38 " --> pdb=" O LYS B 198 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 200 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.863A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.988A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.777A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.849A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.746A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.561A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.708A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.774A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.498A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 143 through 148 376 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: 2.26 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2405 1.34 - 1.46: 2223 1.46 - 1.59: 3702 1.59 - 1.71: 0 1.71 - 1.84: 76 Bond restraints: 8406 Sorted by residual: bond pdb=" C18 U9I A 501 " pdb=" N3 U9I A 501 " ideal model delta sigma weight residual 1.622 1.462 0.160 2.00e-02 2.50e+03 6.42e+01 bond pdb=" C17 U9I A 501 " pdb=" C18 U9I A 501 " ideal model delta sigma weight residual 1.351 1.505 -0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" C5 U9I A 501 " pdb=" N2 U9I A 501 " ideal model delta sigma weight residual 1.497 1.355 0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" C15 U9I A 501 " pdb=" N3 U9I A 501 " ideal model delta sigma weight residual 1.334 1.464 -0.130 2.00e-02 2.50e+03 4.20e+01 bond pdb=" C2 U9I A 501 " pdb=" N1 U9I A 501 " ideal model delta sigma weight residual 1.432 1.348 0.084 2.00e-02 2.50e+03 1.75e+01 ... (remaining 8401 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.25: 155 106.25 - 113.24: 4633 113.24 - 120.23: 2951 120.23 - 127.23: 3616 127.23 - 134.22: 74 Bond angle restraints: 11429 Sorted by residual: angle pdb=" CA THR E 198 " pdb=" CB THR E 198 " pdb=" CG2 THR E 198 " ideal model delta sigma weight residual 110.50 116.12 -5.62 1.70e+00 3.46e-01 1.09e+01 angle pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.77e+00 angle pdb=" C ARG B 313 " pdb=" N ASN B 314 " pdb=" CA ASN B 314 " ideal model delta sigma weight residual 122.82 126.98 -4.16 1.42e+00 4.96e-01 8.59e+00 angle pdb=" N1 U9I A 501 " pdb=" C2 U9I A 501 " pdb=" O1 U9I A 501 " ideal model delta sigma weight residual 119.89 111.30 8.59 3.00e+00 1.11e-01 8.21e+00 angle pdb=" CA CYS A 210 " pdb=" CB CYS A 210 " pdb=" SG CYS A 210 " ideal model delta sigma weight residual 114.40 120.85 -6.45 2.30e+00 1.89e-01 7.86e+00 ... (remaining 11424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.19: 4796 29.19 - 58.37: 124 58.37 - 87.56: 14 87.56 - 116.74: 3 116.74 - 145.92: 1 Dihedral angle restraints: 4938 sinusoidal: 1749 harmonic: 3189 Sorted by residual: dihedral pdb=" CA GLN B 240 " pdb=" C GLN B 240 " pdb=" N THR B 241 " pdb=" CA THR B 241 " ideal model delta harmonic sigma weight residual -180.00 -156.99 -23.01 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" C19 U9I A 501 " pdb=" C13 U9I A 501 " pdb=" C14 U9I A 501 " pdb=" N3 U9I A 501 " ideal model delta sinusoidal sigma weight residual 300.74 154.82 145.92 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" CA THR E 160 " pdb=" C THR E 160 " pdb=" N TYR E 161 " pdb=" CA TYR E 161 " ideal model delta harmonic sigma weight residual -180.00 -158.91 -21.09 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 4935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 906 0.044 - 0.089: 329 0.089 - 0.133: 107 0.133 - 0.177: 11 0.177 - 0.222: 3 Chirality restraints: 1356 Sorted by residual: chirality pdb=" CG LEU C 284 " pdb=" CB LEU C 284 " pdb=" CD1 LEU C 284 " pdb=" CD2 LEU C 284 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CG LEU E 162 " pdb=" CB LEU E 162 " pdb=" CD1 LEU E 162 " pdb=" CD2 LEU E 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C13 U9I A 501 " pdb=" C14 U9I A 501 " pdb=" C19 U9I A 501 " pdb=" N2 U9I A 501 " both_signs ideal model delta sigma weight residual False 2.63 2.43 0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 1353 not shown) Planarity restraints: 1425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 U9I A 501 " -0.039 2.00e-02 2.50e+03 3.99e-02 2.38e+01 pdb=" C4 U9I A 501 " 0.053 2.00e-02 2.50e+03 pdb=" C5 U9I A 501 " -0.003 2.00e-02 2.50e+03 pdb=" C6 U9I A 501 " -0.043 2.00e-02 2.50e+03 pdb=" N2 U9I A 501 " -0.021 2.00e-02 2.50e+03 pdb=" O3 U9I A 501 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 198 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C THR E 198 " -0.056 2.00e-02 2.50e+03 pdb=" O THR E 198 " 0.021 2.00e-02 2.50e+03 pdb=" N ALA E 199 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 337 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.38e+00 pdb=" C PHE B 337 " -0.036 2.00e-02 2.50e+03 pdb=" O PHE B 337 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP B 338 " 0.012 2.00e-02 2.50e+03 ... (remaining 1422 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1820 2.78 - 3.31: 7411 3.31 - 3.84: 13682 3.84 - 4.37: 16364 4.37 - 4.90: 28234 Nonbonded interactions: 67511 Sorted by model distance: nonbonded pdb=" OG SER C 331 " pdb=" OD2 ASP C 333 " model vdw 2.253 2.440 nonbonded pdb=" O VAL A 60 " pdb=" OG1 THR A 63 " model vdw 2.257 2.440 nonbonded pdb=" OH TYR A 66 " pdb=" O TYR A 313 " model vdw 2.283 2.440 nonbonded pdb=" O THR A 150 " pdb=" OG SER A 153 " model vdw 2.291 2.440 nonbonded pdb=" OG SER E 149 " pdb=" O LYS E 151 " model vdw 2.305 2.440 ... (remaining 67506 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.200 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: 5.220 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.540 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 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 : 0.006 0.160 8406 Z= 0.381 Angle : 0.775 10.541 11429 Z= 0.401 Chirality : 0.050 0.222 1356 Planarity : 0.005 0.050 1425 Dihedral : 13.941 145.924 2870 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.12 % Allowed : 0.47 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.00 (0.24), residues: 1074 helix: -0.31 (0.26), residues: 348 sheet: -0.18 (0.29), residues: 294 loop : -1.17 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 63 HIS 0.007 0.001 HIS C 62 PHE 0.030 0.002 PHE A 169 TYR 0.014 0.002 TYR E 178 ARG 0.005 0.000 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 177 time to evaluate : 0.920 Fit side-chains REVERT: C 188 MET cc_start: 0.8086 (mmp) cc_final: 0.7526 (mmm) REVERT: E 219 GLN cc_start: 0.8650 (pp30) cc_final: 0.8443 (pp30) outliers start: 1 outliers final: 1 residues processed: 177 average time/residue: 0.9785 time to fit residues: 186.5286 Evaluate side-chains 172 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 0.2980 chunk 85 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 0.0170 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN E 82 GLN E 174 GLN ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8406 Z= 0.164 Angle : 0.522 7.499 11429 Z= 0.272 Chirality : 0.042 0.139 1356 Planarity : 0.003 0.038 1425 Dihedral : 8.310 163.060 1185 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.01 % Allowed : 10.63 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 (0.25), residues: 1074 helix: 0.55 (0.27), residues: 353 sheet: -0.19 (0.29), residues: 298 loop : -1.07 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE C 253 TYR 0.012 0.001 TYR E 178 ARG 0.004 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 169 time to evaluate : 0.800 Fit side-chains REVERT: C 49 ARG cc_start: 0.8374 (mpt180) cc_final: 0.8148 (mpt180) REVERT: E 219 GLN cc_start: 0.8653 (pp30) cc_final: 0.8451 (pp30) outliers start: 17 outliers final: 4 residues processed: 172 average time/residue: 1.0063 time to fit residues: 185.6402 Evaluate side-chains 171 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 133 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 82 optimal weight: 0.0020 chunk 67 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 314 ASN C 237 ASN C 239 ASN ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN D 59 ASN E 77 ASN E 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8406 Z= 0.228 Angle : 0.545 6.945 11429 Z= 0.284 Chirality : 0.043 0.160 1356 Planarity : 0.003 0.037 1425 Dihedral : 8.164 167.203 1183 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.48 % Allowed : 13.58 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.39 (0.25), residues: 1074 helix: 0.65 (0.27), residues: 363 sheet: -0.13 (0.29), residues: 292 loop : -1.07 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.004 0.001 HIS A 291 PHE 0.011 0.001 PHE A 70 TYR 0.012 0.001 TYR E 178 ARG 0.006 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 177 time to evaluate : 0.821 Fit side-chains REVERT: C 50 THR cc_start: 0.8546 (t) cc_final: 0.8321 (m) REVERT: C 188 MET cc_start: 0.8157 (mmp) cc_final: 0.7407 (mmp) outliers start: 21 outliers final: 15 residues processed: 178 average time/residue: 1.0090 time to fit residues: 192.7449 Evaluate side-chains 184 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 169 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN B 256 ASN B 257 ASN B 312 ASN ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN E 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8406 Z= 0.399 Angle : 0.630 7.662 11429 Z= 0.330 Chirality : 0.047 0.195 1356 Planarity : 0.004 0.044 1425 Dihedral : 8.475 164.821 1183 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.95 % Allowed : 15.58 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.25), residues: 1074 helix: 0.39 (0.27), residues: 362 sheet: -0.31 (0.29), residues: 294 loop : -1.10 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 63 HIS 0.006 0.002 HIS E 220 PHE 0.018 0.002 PHE A 293 TYR 0.016 0.002 TYR A 313 ARG 0.006 0.001 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 182 time to evaluate : 0.949 Fit side-chains REVERT: B 254 ILE cc_start: 0.8370 (mm) cc_final: 0.8141 (mp) REVERT: C 50 THR cc_start: 0.8583 (t) cc_final: 0.8368 (m) REVERT: C 304 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6844 (mtp-110) outliers start: 25 outliers final: 16 residues processed: 186 average time/residue: 1.0115 time to fit residues: 202.1510 Evaluate side-chains 190 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 173 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN B 256 ASN B 257 ASN B 312 ASN ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN E 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8406 Z= 0.256 Angle : 0.573 8.882 11429 Z= 0.298 Chirality : 0.044 0.187 1356 Planarity : 0.003 0.040 1425 Dihedral : 8.379 173.925 1183 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.78 % Allowed : 15.58 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.25), residues: 1074 helix: 0.57 (0.27), residues: 362 sheet: -0.30 (0.29), residues: 295 loop : -1.07 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 169 HIS 0.004 0.001 HIS E 35 PHE 0.012 0.002 PHE C 253 TYR 0.013 0.001 TYR E 178 ARG 0.006 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 174 time to evaluate : 0.875 Fit side-chains REVERT: C 50 THR cc_start: 0.8580 (t) cc_final: 0.8358 (m) outliers start: 32 outliers final: 23 residues processed: 183 average time/residue: 0.9956 time to fit residues: 195.9157 Evaluate side-chains 197 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 174 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 0.0030 chunk 26 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN B 256 ASN B 312 ASN ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN E 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8406 Z= 0.224 Angle : 0.547 9.203 11429 Z= 0.286 Chirality : 0.043 0.180 1356 Planarity : 0.003 0.039 1425 Dihedral : 8.271 178.180 1183 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.83 % Allowed : 17.95 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.40 (0.26), residues: 1074 helix: 0.69 (0.28), residues: 362 sheet: -0.26 (0.29), residues: 296 loop : -1.02 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE C 253 TYR 0.013 0.001 TYR E 178 ARG 0.005 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 0.973 Fit side-chains REVERT: A 151 MET cc_start: 0.6535 (mmm) cc_final: 0.6310 (tmm) REVERT: C 50 THR cc_start: 0.8556 (t) cc_final: 0.8339 (m) REVERT: E 211 ASP cc_start: 0.7352 (m-30) cc_final: 0.7116 (m-30) outliers start: 24 outliers final: 21 residues processed: 178 average time/residue: 0.9613 time to fit residues: 183.9422 Evaluate side-chains 191 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN B 256 ASN ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8406 Z= 0.254 Angle : 0.562 10.104 11429 Z= 0.292 Chirality : 0.044 0.171 1356 Planarity : 0.003 0.038 1425 Dihedral : 8.079 171.102 1183 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.60 % Allowed : 19.01 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.38 (0.26), residues: 1074 helix: 0.70 (0.28), residues: 362 sheet: -0.24 (0.29), residues: 295 loop : -1.01 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 169 HIS 0.004 0.001 HIS E 35 PHE 0.011 0.002 PHE C 278 TYR 0.012 0.001 TYR E 178 ARG 0.007 0.001 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 171 time to evaluate : 0.825 Fit side-chains REVERT: A 151 MET cc_start: 0.6577 (mmm) cc_final: 0.6337 (tmm) REVERT: B 198 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7742 (tttm) REVERT: C 50 THR cc_start: 0.8480 (t) cc_final: 0.8272 (m) REVERT: C 289 TYR cc_start: 0.8585 (m-80) cc_final: 0.8297 (m-80) REVERT: E 211 ASP cc_start: 0.7349 (m-30) cc_final: 0.7105 (m-30) outliers start: 22 outliers final: 22 residues processed: 174 average time/residue: 0.9909 time to fit residues: 185.5154 Evaluate side-chains 195 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 172 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 91 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8406 Z= 0.227 Angle : 0.545 9.511 11429 Z= 0.284 Chirality : 0.043 0.143 1356 Planarity : 0.003 0.037 1425 Dihedral : 7.773 162.367 1183 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.95 % Allowed : 19.24 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.37 (0.26), residues: 1074 helix: 0.78 (0.28), residues: 362 sheet: -0.28 (0.29), residues: 297 loop : -1.03 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.010 0.001 PHE C 278 TYR 0.012 0.001 TYR E 178 ARG 0.005 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 0.952 Fit side-chains REVERT: A 151 MET cc_start: 0.6594 (mmm) cc_final: 0.6355 (mmm) REVERT: B 198 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7759 (tttm) REVERT: C 289 TYR cc_start: 0.8537 (m-80) cc_final: 0.8307 (m-80) REVERT: E 211 ASP cc_start: 0.7349 (m-30) cc_final: 0.7108 (m-30) outliers start: 25 outliers final: 20 residues processed: 174 average time/residue: 0.9851 time to fit residues: 184.3156 Evaluate side-chains 189 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 88 optimal weight: 0.2980 chunk 92 optimal weight: 0.0670 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8406 Z= 0.183 Angle : 0.538 11.959 11429 Z= 0.276 Chirality : 0.042 0.133 1356 Planarity : 0.003 0.036 1425 Dihedral : 7.502 157.127 1183 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.24 % Allowed : 19.95 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.29 (0.26), residues: 1074 helix: 0.87 (0.28), residues: 362 sheet: -0.24 (0.29), residues: 295 loop : -1.02 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE A 70 TYR 0.025 0.001 TYR A 320 ARG 0.004 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 0.814 Fit side-chains REVERT: A 151 MET cc_start: 0.6614 (mmm) cc_final: 0.6363 (mmm) REVERT: B 198 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7778 (tttm) REVERT: B 335 PHE cc_start: 0.8227 (t80) cc_final: 0.7947 (t80) REVERT: C 289 TYR cc_start: 0.8496 (m-80) cc_final: 0.8287 (m-80) outliers start: 19 outliers final: 15 residues processed: 168 average time/residue: 0.9609 time to fit residues: 174.0074 Evaluate side-chains 183 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 167 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 133 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.0370 chunk 86 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 92 optimal weight: 0.0060 chunk 26 optimal weight: 0.4980 overall best weight: 0.3474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN B 270 ASN ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8406 Z= 0.156 Angle : 0.512 9.129 11429 Z= 0.265 Chirality : 0.041 0.134 1356 Planarity : 0.003 0.037 1425 Dihedral : 7.307 155.883 1183 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.89 % Allowed : 20.54 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.15 (0.26), residues: 1074 helix: 1.10 (0.28), residues: 352 sheet: -0.19 (0.29), residues: 296 loop : -0.96 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 211 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE A 70 TYR 0.026 0.001 TYR A 320 ARG 0.004 0.000 ARG E 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 170 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 151 MET cc_start: 0.6620 (mmm) cc_final: 0.6375 (mmm) REVERT: B 198 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7784 (tttm) REVERT: B 335 PHE cc_start: 0.8206 (t80) cc_final: 0.7899 (t80) REVERT: C 312 ASP cc_start: 0.7257 (p0) cc_final: 0.7026 (p0) REVERT: E 180 MET cc_start: 0.7104 (ttp) cc_final: 0.6723 (tmm) outliers start: 16 outliers final: 13 residues processed: 174 average time/residue: 0.9513 time to fit residues: 178.6333 Evaluate side-chains 181 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 167 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 84 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.1980 chunk 76 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.145732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.131229 restraints weight = 11584.850| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.65 r_work: 0.3622 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8406 Z= 0.209 Angle : 0.556 12.719 11429 Z= 0.284 Chirality : 0.042 0.136 1356 Planarity : 0.003 0.037 1425 Dihedral : 7.464 158.757 1183 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.42 % Allowed : 21.25 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.18 (0.26), residues: 1074 helix: 1.02 (0.28), residues: 354 sheet: -0.17 (0.29), residues: 294 loop : -0.96 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE A 70 TYR 0.024 0.002 TYR A 320 ARG 0.003 0.000 ARG C 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3685.44 seconds wall clock time: 66 minutes 10.13 seconds (3970.13 seconds total)