Starting phenix.real_space_refine on Sat Apr 6 10:03:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jer_36193/04_2024/8jer_36193_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jer_36193/04_2024/8jer_36193.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jer_36193/04_2024/8jer_36193_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jer_36193/04_2024/8jer_36193_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jer_36193/04_2024/8jer_36193_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jer_36193/04_2024/8jer_36193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jer_36193/04_2024/8jer_36193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jer_36193/04_2024/8jer_36193_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jer_36193/04_2024/8jer_36193_updated.pdb" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 5008 2.51 5 N 1384 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ASP 201": "OD1" <-> "OD2" Residue "A ASP 218": "OD1" <-> "OD2" Residue "A ASP 252": "OD1" <-> "OD2" Residue "A ASP 273": "OD1" <-> "OD2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 220": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7907 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1531 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 4, 'TRANS': 201} Chain breaks: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2396 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 114 Chain: "R" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 1927 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 277} Chain breaks: 2 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 601 Unresolved non-hydrogen dihedrals: 406 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 4, 'HIS:plan': 3, 'PHE:plan': 14, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 267 Chain: "G" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 384 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1658 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'OJX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.92, per 1000 atoms: 0.62 Number of scatterers: 7907 At special positions: 0 Unit cell: (132.797, 120.725, 87.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 1470 8.00 N 1384 7.00 C 5008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 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: 3.19 Conformation dependent library (CDL) restraints added in 1.8 seconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2090 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 12 sheets defined 32.7% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 9 through 31 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'A' and resid 272 through 281 Processing helix chain 'A' and resid 297 through 311 removed outlier: 3.879A pdb=" N LYS A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 350 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.236A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 51 Proline residue: R 31 - end of helix removed outlier: 3.821A pdb=" N LEU R 47 " --> pdb=" O LEU R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 88 removed outlier: 3.508A pdb=" N LEU R 80 " --> pdb=" O LEU R 76 " (cutoff:3.500A) Proline residue: R 81 - end of helix removed outlier: 3.537A pdb=" N ASN R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 129 Processing helix chain 'R' and resid 135 through 138 Processing helix chain 'R' and resid 141 through 162 removed outlier: 4.985A pdb=" N HIS R 161 " --> pdb=" O GLY R 157 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU R 162 " --> pdb=" O LEU R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 217 removed outlier: 3.927A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 200 - end of helix Processing helix chain 'R' and resid 226 through 261 removed outlier: 3.736A pdb=" N ALA R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 269 through 294 removed outlier: 3.536A pdb=" N PHE R 277 " --> pdb=" O ASP R 273 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR R 283 " --> pdb=" O THR R 279 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR R 284 " --> pdb=" O LEU R 280 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER R 287 " --> pdb=" O THR R 283 " (cutoff:3.500A) Proline residue: R 291 - end of helix removed outlier: 3.622A pdb=" N TYR R 294 " --> pdb=" O ASP R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 302 No H-bonds generated for 'chain 'R' and resid 299 through 302' Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.665A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 7.796A pdb=" N ILE A 265 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N HIS A 322 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU A 267 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS A 225 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N HIS A 196 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU A 36 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ARG A 198 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU A 38 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE A 200 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N GLY A 40 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.510A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.652A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.070A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.702A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 198 through 203 removed outlier: 3.692A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.783A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 294 through 298 removed outlier: 4.252A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.968A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 155 through 159 removed outlier: 3.950A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR H 213 " --> pdb=" O SER H 206 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 243 through 245 removed outlier: 6.083A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1002 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: 2.19 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2622 1.34 - 1.46: 1819 1.46 - 1.58: 3570 1.58 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 8069 Sorted by residual: bond pdb=" C LYS R 15 " pdb=" N LYS R 16 " ideal model delta sigma weight residual 1.331 1.233 0.098 1.30e-02 5.92e+03 5.72e+01 bond pdb=" CA ILE R 98 " pdb=" CB ILE R 98 " ideal model delta sigma weight residual 1.539 1.521 0.018 5.40e-03 3.43e+04 1.15e+01 bond pdb=" N GLY R 173 " pdb=" CA GLY R 173 " ideal model delta sigma weight residual 1.446 1.484 -0.038 1.33e-02 5.65e+03 8.30e+00 bond pdb=" N PHE R 277 " pdb=" CA PHE R 277 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.20e-02 6.94e+03 5.07e+00 bond pdb=" N PHE R 186 " pdb=" CA PHE R 186 " ideal model delta sigma weight residual 1.462 1.489 -0.027 1.38e-02 5.25e+03 3.94e+00 ... (remaining 8064 not shown) Histogram of bond angle deviations from ideal: 100.09 - 107.06: 188 107.06 - 114.04: 4594 114.04 - 121.01: 3769 121.01 - 127.99: 2394 127.99 - 134.97: 70 Bond angle restraints: 11015 Sorted by residual: angle pdb=" N PRO R 31 " pdb=" CA PRO R 31 " pdb=" C PRO R 31 " ideal model delta sigma weight residual 110.70 117.41 -6.71 1.22e+00 6.72e-01 3.02e+01 angle pdb=" CA PRO R 31 " pdb=" C PRO R 31 " pdb=" N PRO R 32 " ideal model delta sigma weight residual 117.93 123.45 -5.52 1.20e+00 6.94e-01 2.12e+01 angle pdb=" N TYR R 284 " pdb=" CA TYR R 284 " pdb=" C TYR R 284 " ideal model delta sigma weight residual 111.36 106.58 4.78 1.09e+00 8.42e-01 1.92e+01 angle pdb=" N VAL H 64 " pdb=" CA VAL H 64 " pdb=" C VAL H 64 " ideal model delta sigma weight residual 113.71 109.62 4.09 9.50e-01 1.11e+00 1.85e+01 angle pdb=" CA LYS R 15 " pdb=" C LYS R 15 " pdb=" N LYS R 16 " ideal model delta sigma weight residual 116.21 110.75 5.46 1.29e+00 6.01e-01 1.79e+01 ... (remaining 11010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4314 17.82 - 35.64: 309 35.64 - 53.46: 60 53.46 - 71.28: 7 71.28 - 89.10: 4 Dihedral angle restraints: 4694 sinusoidal: 1463 harmonic: 3231 Sorted by residual: dihedral pdb=" CB CYS R 19 " pdb=" SG CYS R 19 " pdb=" SG CYS R 266 " pdb=" CB CYS R 266 " ideal model delta sinusoidal sigma weight residual 93.00 171.24 -78.24 1 1.00e+01 1.00e-02 7.64e+01 dihedral pdb=" CB CYS R 100 " pdb=" SG CYS R 100 " pdb=" SG CYS R 177 " pdb=" CB CYS R 177 " ideal model delta sinusoidal sigma weight residual 93.00 123.58 -30.58 1 1.00e+01 1.00e-02 1.34e+01 dihedral pdb=" CA ASP B 258 " pdb=" C ASP B 258 " pdb=" N GLN B 259 " pdb=" CA GLN B 259 " ideal model delta harmonic sigma weight residual 180.00 163.88 16.12 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 4691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1044 0.053 - 0.106: 212 0.106 - 0.159: 33 0.159 - 0.211: 1 0.211 - 0.264: 2 Chirality restraints: 1292 Sorted by residual: chirality pdb=" CB ILE R 182 " pdb=" CA ILE R 182 " pdb=" CG1 ILE R 182 " pdb=" CG2 ILE R 182 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA PRO R 31 " pdb=" N PRO R 31 " pdb=" C PRO R 31 " pdb=" CB PRO R 31 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB THR H 91 " pdb=" CA THR H 91 " pdb=" OG1 THR H 91 " pdb=" CG2 THR H 91 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.32e-01 ... (remaining 1289 not shown) Planarity restraints: 1423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN R 170 " 0.023 2.00e-02 2.50e+03 4.62e-02 2.14e+01 pdb=" C GLN R 170 " -0.080 2.00e-02 2.50e+03 pdb=" O GLN R 170 " 0.031 2.00e-02 2.50e+03 pdb=" N ASN R 171 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP R 290 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO R 291 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO R 291 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 291 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 14 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C ASP R 14 " -0.034 2.00e-02 2.50e+03 pdb=" O ASP R 14 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS R 15 " 0.011 2.00e-02 2.50e+03 ... (remaining 1420 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 908 2.75 - 3.29: 7766 3.29 - 3.82: 12669 3.82 - 4.36: 14065 4.36 - 4.90: 25968 Nonbonded interactions: 61376 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.211 2.440 nonbonded pdb=" O LEU R 66 " pdb=" OH TYR R 294 " model vdw 2.223 2.440 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.242 2.440 nonbonded pdb=" O ARG H 67 " pdb=" OG1 THR H 84 " model vdw 2.267 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.285 2.440 ... (remaining 61371 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: 1.400 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: 5.470 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.090 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 8069 Z= 0.239 Angle : 0.616 9.966 11015 Z= 0.355 Chirality : 0.044 0.264 1292 Planarity : 0.004 0.049 1423 Dihedral : 12.986 89.102 2589 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.14 % Allowed : 0.28 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.23 (0.27), residues: 1097 helix: 1.74 (0.29), residues: 352 sheet: -1.14 (0.31), residues: 283 loop : -0.08 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE B 151 TYR 0.013 0.001 TYR H 190 ARG 0.008 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6920 (tm-30) REVERT: A 208 GLU cc_start: 0.7168 (tp30) cc_final: 0.6641 (tt0) REVERT: B 273 ILE cc_start: 0.8113 (mp) cc_final: 0.7897 (mt) REVERT: R 109 MET cc_start: 0.6415 (tmm) cc_final: 0.6053 (ttp) REVERT: R 131 HIS cc_start: 0.8438 (m-70) cc_final: 0.8088 (m-70) REVERT: R 186 PHE cc_start: 0.6540 (OUTLIER) cc_final: 0.6268 (t80) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.2109 time to fit residues: 51.2020 Evaluate side-chains 142 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 186 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 85 optimal weight: 0.0370 chunk 33 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 347 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 175 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8069 Z= 0.211 Angle : 0.540 9.195 11015 Z= 0.291 Chirality : 0.044 0.145 1292 Planarity : 0.004 0.063 1423 Dihedral : 4.629 88.837 1185 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.83 % Allowed : 9.72 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.30 (0.26), residues: 1097 helix: 1.92 (0.28), residues: 350 sheet: -1.08 (0.30), residues: 293 loop : -0.13 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.003 0.001 HIS H 35 PHE 0.015 0.001 PHE H 68 TYR 0.016 0.001 TYR A 297 ARG 0.005 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 155 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7170 (tp30) cc_final: 0.6616 (tt0) REVERT: A 256 ASN cc_start: 0.8734 (m-40) cc_final: 0.8524 (m-40) REVERT: A 320 TYR cc_start: 0.8811 (m-80) cc_final: 0.8386 (m-80) REVERT: B 273 ILE cc_start: 0.8199 (mp) cc_final: 0.7919 (mt) REVERT: R 11 LEU cc_start: 0.6181 (tt) cc_final: 0.5913 (tt) REVERT: R 109 MET cc_start: 0.6417 (tmm) cc_final: 0.6180 (ttp) REVERT: R 131 HIS cc_start: 0.8382 (m-70) cc_final: 0.7999 (m-70) REVERT: R 186 PHE cc_start: 0.6538 (OUTLIER) cc_final: 0.6265 (t80) outliers start: 13 outliers final: 10 residues processed: 164 average time/residue: 0.2130 time to fit residues: 46.3387 Evaluate side-chains 152 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 141 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain R residue 171 ASN Chi-restraints excluded: chain R residue 186 PHE Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 149 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.0030 chunk 30 optimal weight: 0.3980 chunk 82 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 40.0000 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 33 optimal weight: 0.0470 chunk 79 optimal weight: 0.9990 overall best weight: 0.3888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8069 Z= 0.160 Angle : 0.488 7.541 11015 Z= 0.260 Chirality : 0.042 0.172 1292 Planarity : 0.004 0.051 1423 Dihedral : 4.471 87.163 1185 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.39 % Allowed : 11.83 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.31 (0.26), residues: 1097 helix: 1.93 (0.28), residues: 351 sheet: -0.97 (0.29), residues: 289 loop : -0.24 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.002 0.000 HIS B 142 PHE 0.012 0.001 PHE H 68 TYR 0.019 0.001 TYR A 297 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7040 (tp30) cc_final: 0.6542 (tt0) REVERT: B 273 ILE cc_start: 0.8134 (mp) cc_final: 0.7865 (mt) REVERT: R 131 HIS cc_start: 0.8307 (m-70) cc_final: 0.7924 (m-70) REVERT: R 134 HIS cc_start: 0.7382 (t-90) cc_final: 0.7151 (t70) REVERT: R 186 PHE cc_start: 0.6571 (OUTLIER) cc_final: 0.6305 (t80) REVERT: H 18 ARG cc_start: 0.7547 (tpp80) cc_final: 0.7146 (ttm170) outliers start: 17 outliers final: 13 residues processed: 164 average time/residue: 0.2001 time to fit residues: 44.4785 Evaluate side-chains 154 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 171 ASN Chi-restraints excluded: chain R residue 186 PHE Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 178 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 30.0000 chunk 105 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN R 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8069 Z= 0.267 Angle : 0.514 7.545 11015 Z= 0.275 Chirality : 0.044 0.147 1292 Planarity : 0.004 0.061 1423 Dihedral : 4.565 85.107 1185 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.46 % Favored : 96.44 % Rotamer: Outliers : 4.23 % Allowed : 13.10 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.20 (0.26), residues: 1097 helix: 1.96 (0.28), residues: 352 sheet: -1.14 (0.29), residues: 298 loop : -0.30 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 36 HIS 0.003 0.001 HIS B 91 PHE 0.014 0.001 PHE B 235 TYR 0.018 0.002 TYR A 297 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 144 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7198 (tp30) cc_final: 0.6970 (tp30) REVERT: A 246 GLU cc_start: 0.6349 (pm20) cc_final: 0.6146 (pm20) REVERT: B 234 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.7948 (m-10) REVERT: B 273 ILE cc_start: 0.8180 (mp) cc_final: 0.7925 (mt) REVERT: R 131 HIS cc_start: 0.8357 (m-70) cc_final: 0.7967 (m-70) REVERT: R 186 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.6378 (t80) REVERT: H 18 ARG cc_start: 0.7569 (tpp80) cc_final: 0.7117 (ttm170) outliers start: 30 outliers final: 20 residues processed: 166 average time/residue: 0.1918 time to fit residues: 43.5800 Evaluate side-chains 165 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 143 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 141 ASN Chi-restraints excluded: chain R residue 171 ASN Chi-restraints excluded: chain R residue 186 PHE Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 199 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8069 Z= 0.237 Angle : 0.495 7.325 11015 Z= 0.265 Chirality : 0.043 0.161 1292 Planarity : 0.004 0.059 1423 Dihedral : 4.527 84.801 1185 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.19 % Favored : 96.72 % Rotamer: Outliers : 4.65 % Allowed : 14.37 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.22 (0.26), residues: 1097 helix: 1.92 (0.29), residues: 353 sheet: -1.06 (0.30), residues: 289 loop : -0.33 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 36 HIS 0.003 0.001 HIS B 91 PHE 0.014 0.001 PHE H 68 TYR 0.019 0.001 TYR A 297 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 148 time to evaluate : 0.887 Fit side-chains REVERT: A 208 GLU cc_start: 0.7170 (tp30) cc_final: 0.6969 (tp30) REVERT: B 234 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.7969 (m-10) REVERT: B 273 ILE cc_start: 0.8180 (mp) cc_final: 0.7928 (mt) REVERT: R 131 HIS cc_start: 0.8332 (m-70) cc_final: 0.7926 (m-70) REVERT: R 186 PHE cc_start: 0.6603 (OUTLIER) cc_final: 0.6334 (t80) REVERT: H 18 ARG cc_start: 0.7563 (tpp80) cc_final: 0.7075 (ttm170) REVERT: H 87 ARG cc_start: 0.6754 (mpt180) cc_final: 0.6528 (mtt90) outliers start: 33 outliers final: 25 residues processed: 172 average time/residue: 0.1919 time to fit residues: 45.0743 Evaluate side-chains 166 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 141 ASN Chi-restraints excluded: chain R residue 171 ASN Chi-restraints excluded: chain R residue 186 PHE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 199 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN R 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8069 Z= 0.269 Angle : 0.517 7.542 11015 Z= 0.274 Chirality : 0.044 0.172 1292 Planarity : 0.004 0.060 1423 Dihedral : 4.611 85.101 1185 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.65 % Favored : 96.26 % Rotamer: Outliers : 4.65 % Allowed : 15.49 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.09 (0.26), residues: 1097 helix: 1.87 (0.29), residues: 353 sheet: -1.19 (0.30), residues: 292 loop : -0.40 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.001 PHE H 27 TYR 0.020 0.002 TYR A 297 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 147 time to evaluate : 0.931 Fit side-chains REVERT: A 208 GLU cc_start: 0.7212 (tp30) cc_final: 0.7010 (tp30) REVERT: B 234 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.7942 (m-10) REVERT: B 273 ILE cc_start: 0.8170 (mp) cc_final: 0.7959 (mt) REVERT: R 118 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8085 (mt) REVERT: R 131 HIS cc_start: 0.8347 (m-70) cc_final: 0.7966 (m-70) REVERT: R 186 PHE cc_start: 0.6576 (OUTLIER) cc_final: 0.6300 (t80) REVERT: H 18 ARG cc_start: 0.7535 (tpp80) cc_final: 0.7056 (ttm170) REVERT: H 87 ARG cc_start: 0.6814 (mpt180) cc_final: 0.6557 (mtt90) outliers start: 33 outliers final: 25 residues processed: 169 average time/residue: 0.1818 time to fit residues: 42.1448 Evaluate side-chains 172 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 144 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 141 ASN Chi-restraints excluded: chain R residue 186 PHE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 199 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 65 optimal weight: 0.3980 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN R 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8069 Z= 0.234 Angle : 0.509 7.785 11015 Z= 0.268 Chirality : 0.043 0.178 1292 Planarity : 0.004 0.061 1423 Dihedral : 4.584 85.621 1185 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.65 % Favored : 96.26 % Rotamer: Outliers : 4.23 % Allowed : 16.48 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.09 (0.26), residues: 1097 helix: 1.89 (0.29), residues: 353 sheet: -1.23 (0.30), residues: 294 loop : -0.38 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.011 0.001 PHE H 68 TYR 0.022 0.001 TYR A 297 ARG 0.004 0.000 ARG R 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 140 time to evaluate : 0.866 Fit side-chains REVERT: B 234 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.7957 (m-10) REVERT: B 273 ILE cc_start: 0.8161 (mp) cc_final: 0.7947 (mt) REVERT: R 131 HIS cc_start: 0.8367 (m-70) cc_final: 0.7994 (m-70) REVERT: R 186 PHE cc_start: 0.6574 (OUTLIER) cc_final: 0.6292 (t80) REVERT: H 18 ARG cc_start: 0.7517 (tpp80) cc_final: 0.7063 (ttm170) REVERT: H 87 ARG cc_start: 0.6769 (mpt180) cc_final: 0.6553 (mtt90) outliers start: 30 outliers final: 23 residues processed: 161 average time/residue: 0.1887 time to fit residues: 41.6586 Evaluate side-chains 166 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 186 PHE Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 199 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 0.0870 chunk 20 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN R 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8069 Z= 0.212 Angle : 0.508 9.925 11015 Z= 0.265 Chirality : 0.043 0.182 1292 Planarity : 0.004 0.062 1423 Dihedral : 4.542 87.440 1185 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.19 % Favored : 96.72 % Rotamer: Outliers : 4.37 % Allowed : 16.62 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.10 (0.26), residues: 1097 helix: 1.91 (0.29), residues: 353 sheet: -1.23 (0.30), residues: 290 loop : -0.39 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 211 HIS 0.002 0.001 HIS B 91 PHE 0.011 0.001 PHE H 68 TYR 0.023 0.001 TYR A 297 ARG 0.004 0.000 ARG R 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 144 time to evaluate : 0.941 Fit side-chains REVERT: A 246 GLU cc_start: 0.5807 (pm20) cc_final: 0.5562 (pm20) REVERT: B 59 TYR cc_start: 0.8662 (m-80) cc_final: 0.8331 (m-80) REVERT: B 198 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7891 (pp) REVERT: B 234 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.7967 (m-10) REVERT: B 273 ILE cc_start: 0.8150 (mp) cc_final: 0.7924 (mt) REVERT: R 131 HIS cc_start: 0.8329 (m-70) cc_final: 0.7977 (m-70) REVERT: R 186 PHE cc_start: 0.6608 (OUTLIER) cc_final: 0.6348 (t80) REVERT: H 18 ARG cc_start: 0.7510 (tpp80) cc_final: 0.7059 (ttm170) outliers start: 31 outliers final: 25 residues processed: 165 average time/residue: 0.2022 time to fit residues: 45.1728 Evaluate side-chains 166 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 141 ASN Chi-restraints excluded: chain R residue 186 PHE Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 199 VAL 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: 0.7980 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 92 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 0.0270 chunk 63 optimal weight: 0.9980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8069 Z= 0.180 Angle : 0.500 8.041 11015 Z= 0.263 Chirality : 0.043 0.182 1292 Planarity : 0.004 0.059 1423 Dihedral : 4.526 88.928 1185 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Rotamer: Outliers : 3.80 % Allowed : 16.90 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 1097 helix: 2.03 (0.29), residues: 347 sheet: -1.22 (0.30), residues: 296 loop : -0.33 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 82 HIS 0.002 0.000 HIS B 142 PHE 0.011 0.001 PHE H 68 TYR 0.023 0.001 TYR A 297 ARG 0.008 0.000 ARG R 216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 0.915 Fit side-chains REVERT: A 246 GLU cc_start: 0.5871 (pm20) cc_final: 0.5622 (pm20) REVERT: B 59 TYR cc_start: 0.8547 (m-80) cc_final: 0.8308 (m-80) REVERT: B 198 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7816 (pp) REVERT: B 234 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.7969 (m-10) REVERT: B 273 ILE cc_start: 0.8131 (mp) cc_final: 0.7912 (mt) REVERT: R 131 HIS cc_start: 0.8228 (m-70) cc_final: 0.7888 (m-70) REVERT: R 186 PHE cc_start: 0.6601 (OUTLIER) cc_final: 0.6336 (t80) REVERT: H 18 ARG cc_start: 0.7512 (tpp80) cc_final: 0.7073 (ttm170) outliers start: 27 outliers final: 23 residues processed: 160 average time/residue: 0.1965 time to fit residues: 42.4930 Evaluate side-chains 166 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 141 ASN Chi-restraints excluded: chain R residue 186 PHE Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 149 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.0770 chunk 71 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 20.0000 chunk 86 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 68 optimal weight: 0.0070 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8069 Z= 0.170 Angle : 0.516 12.354 11015 Z= 0.264 Chirality : 0.043 0.185 1292 Planarity : 0.004 0.056 1423 Dihedral : 4.537 89.306 1185 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.37 % Favored : 96.54 % Rotamer: Outliers : 3.80 % Allowed : 17.18 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.21 (0.27), residues: 1097 helix: 2.04 (0.29), residues: 347 sheet: -1.12 (0.30), residues: 292 loop : -0.36 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 36 HIS 0.002 0.000 HIS B 142 PHE 0.010 0.001 PHE R 117 TYR 0.028 0.001 TYR A 297 ARG 0.007 0.000 ARG R 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 145 time to evaluate : 0.951 Fit side-chains REVERT: A 246 GLU cc_start: 0.5773 (pm20) cc_final: 0.5558 (pm20) REVERT: B 198 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7798 (pp) REVERT: B 234 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8036 (m-10) REVERT: B 273 ILE cc_start: 0.8157 (mp) cc_final: 0.7923 (mt) REVERT: R 11 LEU cc_start: 0.6779 (tt) cc_final: 0.6564 (tt) REVERT: R 109 MET cc_start: 0.6285 (tpt) cc_final: 0.5963 (tpt) REVERT: R 131 HIS cc_start: 0.8203 (m-70) cc_final: 0.7887 (m-70) REVERT: R 186 PHE cc_start: 0.6563 (OUTLIER) cc_final: 0.6300 (t80) REVERT: R 251 ARG cc_start: 0.7923 (tpt-90) cc_final: 0.7709 (tpp80) REVERT: H 18 ARG cc_start: 0.7467 (tpp80) cc_final: 0.6998 (ttm170) outliers start: 27 outliers final: 23 residues processed: 162 average time/residue: 0.2010 time to fit residues: 44.5972 Evaluate side-chains 166 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 141 ASN Chi-restraints excluded: chain R residue 186 PHE Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 149 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 86 optimal weight: 0.0570 chunk 36 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.195588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.151804 restraints weight = 9526.025| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.79 r_work: 0.3510 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8069 Z= 0.242 Angle : 0.535 12.029 11015 Z= 0.277 Chirality : 0.044 0.182 1292 Planarity : 0.004 0.056 1423 Dihedral : 4.589 88.304 1185 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.65 % Favored : 96.26 % Rotamer: Outliers : 4.37 % Allowed : 16.62 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.10 (0.27), residues: 1097 helix: 2.01 (0.29), residues: 347 sheet: -1.29 (0.30), residues: 299 loop : -0.37 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE H 27 TYR 0.028 0.002 TYR A 297 ARG 0.008 0.000 ARG R 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2087.43 seconds wall clock time: 38 minutes 35.22 seconds (2315.22 seconds total)