Starting phenix.real_space_refine on Mon Mar 11 12:21:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/03_2024/8w87_37347_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/03_2024/8w87_37347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/03_2024/8w87_37347.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/03_2024/8w87_37347.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/03_2024/8w87_37347_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/03_2024/8w87_37347_neut_updated.pdb" } resolution = 2.8 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= 0.047 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 63 5.16 5 C 5235 2.51 5 N 1415 2.21 5 O 1515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 224": "OD1" <-> "OD2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ASP 352": "OD1" <-> "OD2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G ASP 48": "OD1" <-> "OD2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 90": "OD1" <-> "OD2" Residue "R ASP 21": "OD1" <-> "OD2" Residue "R PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 86": "OE1" <-> "OE2" Residue "R TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 8228 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1906 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2315 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'B40': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.90, per 1000 atoms: 0.60 Number of scatterers: 8228 At special positions: 0 Unit cell: (82.4, 98.88, 132.664, 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 63 16.00 O 1515 8.00 N 1415 7.00 C 5235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.26 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: 3.28 Conformation dependent library (CDL) restraints added in 1.5 seconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB B40 R 501 " Number of C-beta restraints generated: 1968 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 10 sheets defined 39.8% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 13 through 34 removed outlier: 3.820A pdb=" N GLU A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 62 removed outlier: 3.934A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.511A pdb=" N PHE A 222 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 252 removed outlier: 4.795A pdb=" N GLN A 241 " --> pdb=" O ASN A 238 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 252 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 277 Processing helix chain 'A' and resid 282 through 285 No H-bonds generated for 'chain 'A' and resid 282 through 285' Processing helix chain 'A' and resid 287 through 290 Processing helix chain 'A' and resid 306 through 325 removed outlier: 3.749A pdb=" N ILE A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 364 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 47 removed outlier: 4.880A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 20 through 50 Processing helix chain 'R' and resid 57 through 75 Processing helix chain 'R' and resid 77 through 86 Processing helix chain 'R' and resid 92 through 126 Processing helix chain 'R' and resid 131 through 134 No H-bonds generated for 'chain 'R' and resid 131 through 134' Processing helix chain 'R' and resid 137 through 161 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 169 through 179 Processing helix chain 'R' and resid 188 through 198 Processing helix chain 'R' and resid 200 through 230 Processing helix chain 'R' and resid 248 through 277 removed outlier: 3.610A pdb=" N PHE R 260 " --> pdb=" O VAL R 256 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 285 through 304 removed outlier: 3.631A pdb=" N SER R 297 " --> pdb=" O GLY R 293 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 309 through 319 Processing sheet with id= A, first strand: chain 'A' and resid 333 through 337 removed outlier: 7.240A pdb=" N VAL A 261 " --> pdb=" O TYR A 334 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N HIS A 336 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU A 263 " --> pdb=" O HIS A 336 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA A 227 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN A 202 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LEU A 43 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N HIS A 204 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU A 45 " --> pdb=" O HIS A 204 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE A 206 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLY A 47 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N VAL A 208 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.808A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.743A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.667A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.802A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.638A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.454A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.556A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.190A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1155 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: 2.51 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1386 1.32 - 1.44: 2303 1.44 - 1.57: 4625 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 8406 Sorted by residual: bond pdb=" C THR R 102 " pdb=" N ASP R 103 " ideal model delta sigma weight residual 1.334 1.415 -0.082 1.23e-02 6.61e+03 4.39e+01 bond pdb=" C ASP R 103 " pdb=" N ILE R 104 " ideal model delta sigma weight residual 1.334 1.258 0.076 1.25e-02 6.40e+03 3.74e+01 bond pdb=" C ASP R 103 " pdb=" O ASP R 103 " ideal model delta sigma weight residual 1.236 1.200 0.036 1.15e-02 7.56e+03 9.89e+00 bond pdb=" CB ASP R 103 " pdb=" CG ASP R 103 " ideal model delta sigma weight residual 1.516 1.459 0.057 2.50e-02 1.60e+03 5.29e+00 bond pdb=" CA ASP R 103 " pdb=" CB ASP R 103 " ideal model delta sigma weight residual 1.530 1.557 -0.027 1.57e-02 4.06e+03 3.05e+00 ... (remaining 8401 not shown) Histogram of bond angle deviations from ideal: 100.49 - 107.21: 222 107.21 - 113.94: 4701 113.94 - 120.67: 3468 120.67 - 127.39: 2904 127.39 - 134.12: 89 Bond angle restraints: 11384 Sorted by residual: angle pdb=" C ASP R 103 " pdb=" CA ASP R 103 " pdb=" CB ASP R 103 " ideal model delta sigma weight residual 110.96 105.05 5.91 1.54e+00 4.22e-01 1.47e+01 angle pdb=" CA B40 R 501 " pdb=" N B40 R 501 " pdb=" CM B40 R 501 " ideal model delta sigma weight residual 115.05 104.23 10.82 3.00e+00 1.11e-01 1.30e+01 angle pdb=" N B40 R 501 " pdb=" CA B40 R 501 " pdb=" C B40 R 501 " ideal model delta sigma weight residual 114.49 104.29 10.20 3.00e+00 1.11e-01 1.16e+01 angle pdb=" N VAL R 150 " pdb=" CA VAL R 150 " pdb=" C VAL R 150 " ideal model delta sigma weight residual 112.35 108.63 3.72 1.20e+00 6.94e-01 9.62e+00 angle pdb=" N SER B 331 " pdb=" CA SER B 331 " pdb=" C SER B 331 " ideal model delta sigma weight residual 108.60 112.56 -3.96 1.46e+00 4.69e-01 7.37e+00 ... (remaining 11379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.64: 4508 19.64 - 39.29: 381 39.29 - 58.93: 79 58.93 - 78.58: 16 78.58 - 98.22: 6 Dihedral angle restraints: 4990 sinusoidal: 1945 harmonic: 3045 Sorted by residual: dihedral pdb=" CA PHE B 292 " pdb=" C PHE B 292 " pdb=" N ASN B 293 " pdb=" CA ASN B 293 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -162.49 -17.51 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CB B40 R 501 " pdb=" N B40 R 501 " pdb=" CA B40 R 501 " pdb=" CM B40 R 501 " ideal model delta sinusoidal sigma weight residual 168.08 -93.70 -98.22 1 3.00e+01 1.11e-03 1.22e+01 ... (remaining 4987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1106 0.056 - 0.113: 144 0.113 - 0.169: 23 0.169 - 0.226: 1 0.226 - 0.282: 1 Chirality restraints: 1275 Sorted by residual: chirality pdb=" CA B40 R 501 " pdb=" N B40 R 501 " pdb=" C B40 R 501 " pdb=" CB B40 R 501 " both_signs ideal model delta sigma weight residual False -2.42 -2.71 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ASP R 103 " pdb=" N ASP R 103 " pdb=" C ASP R 103 " pdb=" CB ASP R 103 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 1272 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 284 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C THR R 284 " -0.059 2.00e-02 2.50e+03 pdb=" O THR R 284 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU R 285 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO R 282 " 0.056 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO R 283 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO R 283 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO R 283 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 19 " -0.182 9.50e-02 1.11e+02 8.20e-02 4.90e+00 pdb=" NE ARG B 19 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 19 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 19 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 19 " -0.002 2.00e-02 2.50e+03 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 602 2.73 - 3.28: 8423 3.28 - 3.82: 13984 3.82 - 4.36: 17323 4.36 - 4.90: 30113 Nonbonded interactions: 70445 Sorted by model distance: nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.193 2.440 nonbonded pdb=" O ASN A 188 " pdb=" OG SER A 189 " model vdw 2.226 2.440 nonbonded pdb=" C B40 R 501 " pdb=" CM B40 R 501 " model vdw 2.251 3.104 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.314 2.440 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.319 2.440 ... (remaining 70440 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: 0.810 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: 0.000 Extract box with map and model: 4.030 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 26.540 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:11.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 8406 Z= 0.224 Angle : 0.561 10.817 11384 Z= 0.318 Chirality : 0.041 0.282 1275 Planarity : 0.005 0.083 1448 Dihedral : 15.674 98.222 3019 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.45 % Allowed : 16.10 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.27), residues: 1031 helix: 2.26 (0.25), residues: 416 sheet: 0.46 (0.34), residues: 228 loop : -0.01 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 291 HIS 0.004 0.001 HIS B 91 PHE 0.011 0.001 PHE R 70 TYR 0.008 0.001 TYR A 313 ARG 0.015 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 330 ARG cc_start: 0.7951 (mtm110) cc_final: 0.7653 (mtm110) REVERT: B 17 GLN cc_start: 0.6251 (tt0) cc_final: 0.6005 (tm130) outliers start: 4 outliers final: 3 residues processed: 130 average time/residue: 1.3063 time to fit residues: 179.9618 Evaluate side-chains 124 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain R residue 80 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.0870 chunk 58 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN N 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8406 Z= 0.237 Angle : 0.522 7.028 11384 Z= 0.282 Chirality : 0.043 0.160 1275 Planarity : 0.004 0.059 1448 Dihedral : 5.603 59.443 1149 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.91 % Allowed : 15.20 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.27), residues: 1031 helix: 2.08 (0.25), residues: 422 sheet: 0.37 (0.34), residues: 220 loop : -0.01 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.004 0.001 HIS A 336 PHE 0.021 0.002 PHE R 165 TYR 0.027 0.001 TYR R 27 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 213 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7969 (p0) REVERT: A 321 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7125 (mtp85) REVERT: A 355 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8266 (t0) REVERT: R 80 SER cc_start: 0.8104 (t) cc_final: 0.7320 (p) outliers start: 17 outliers final: 4 residues processed: 138 average time/residue: 1.3182 time to fit residues: 192.4202 Evaluate side-chains 128 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 64 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 0.0770 chunk 76 optimal weight: 9.9990 chunk 62 optimal weight: 0.0000 chunk 25 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.7146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN N 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8406 Z= 0.161 Angle : 0.467 5.658 11384 Z= 0.253 Chirality : 0.041 0.153 1275 Planarity : 0.004 0.052 1448 Dihedral : 4.993 55.191 1148 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.03 % Allowed : 16.44 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.27), residues: 1031 helix: 2.02 (0.25), residues: 424 sheet: 0.45 (0.34), residues: 223 loop : 0.10 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.003 0.001 HIS G 44 PHE 0.013 0.001 PHE A 196 TYR 0.022 0.001 TYR R 27 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 0.965 Fit side-chains REVERT: A 200 LYS cc_start: 0.8933 (mttp) cc_final: 0.8641 (mmtm) REVERT: A 213 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7939 (p0) REVERT: A 321 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7082 (mtp85) REVERT: A 355 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8240 (t0) REVERT: R 80 SER cc_start: 0.8161 (t) cc_final: 0.7343 (p) REVERT: R 135 MET cc_start: 0.8672 (mmp) cc_final: 0.8419 (mmt) outliers start: 18 outliers final: 8 residues processed: 144 average time/residue: 1.1997 time to fit residues: 184.0937 Evaluate side-chains 132 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8406 Z= 0.255 Angle : 0.504 6.575 11384 Z= 0.270 Chirality : 0.043 0.154 1275 Planarity : 0.004 0.050 1448 Dihedral : 5.210 59.152 1148 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.27 % Allowed : 16.78 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.26), residues: 1031 helix: 1.80 (0.25), residues: 430 sheet: 0.37 (0.34), residues: 226 loop : -0.01 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 218 HIS 0.004 0.001 HIS G 44 PHE 0.017 0.002 PHE R 165 TYR 0.009 0.001 TYR A 313 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 200 LYS cc_start: 0.8940 (mttp) cc_final: 0.8645 (mmtm) REVERT: A 213 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8019 (p0) REVERT: A 321 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7149 (mtp85) REVERT: A 355 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8267 (t0) REVERT: B 175 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7906 (mp10) REVERT: N 108 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.8263 (m-80) REVERT: R 51 PHE cc_start: 0.7705 (m-80) cc_final: 0.7420 (m-80) REVERT: R 80 SER cc_start: 0.8171 (t) cc_final: 0.7316 (p) outliers start: 29 outliers final: 12 residues processed: 151 average time/residue: 1.2173 time to fit residues: 195.4223 Evaluate side-chains 143 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 0.0870 chunk 40 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8406 Z= 0.190 Angle : 0.470 5.710 11384 Z= 0.254 Chirality : 0.041 0.148 1275 Planarity : 0.004 0.049 1448 Dihedral : 5.034 56.218 1148 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.15 % Allowed : 17.34 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.26), residues: 1031 helix: 1.82 (0.25), residues: 430 sheet: 0.45 (0.34), residues: 223 loop : -0.08 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.003 0.001 HIS R 63 PHE 0.013 0.001 PHE A 196 TYR 0.013 0.001 TYR R 27 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 0.945 Fit side-chains REVERT: A 58 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8014 (mptt) REVERT: A 200 LYS cc_start: 0.8939 (mttp) cc_final: 0.8670 (mmtm) REVERT: A 213 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7980 (p0) REVERT: A 321 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7118 (mtp85) REVERT: A 330 ARG cc_start: 0.7820 (mtm110) cc_final: 0.7441 (mtm110) REVERT: A 355 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8234 (t0) REVERT: B 175 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7925 (mp10) REVERT: B 214 ARG cc_start: 0.8237 (mmm-85) cc_final: 0.7727 (mpp80) REVERT: B 259 GLN cc_start: 0.7847 (tt0) cc_final: 0.7089 (pt0) REVERT: R 51 PHE cc_start: 0.7702 (m-80) cc_final: 0.7420 (m-80) REVERT: R 80 SER cc_start: 0.8149 (t) cc_final: 0.7301 (p) REVERT: R 91 PHE cc_start: 0.7376 (m-80) cc_final: 0.7107 (m-80) REVERT: R 135 MET cc_start: 0.8737 (mmp) cc_final: 0.8501 (mmt) outliers start: 28 outliers final: 17 residues processed: 151 average time/residue: 1.1830 time to fit residues: 190.2714 Evaluate side-chains 150 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 128 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 271 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1389 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= 0.193 Angle : 0.472 5.557 11384 Z= 0.254 Chirality : 0.041 0.148 1275 Planarity : 0.004 0.049 1448 Dihedral : 4.935 55.283 1148 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.49 % Allowed : 17.12 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.26), residues: 1031 helix: 1.82 (0.26), residues: 430 sheet: 0.44 (0.34), residues: 223 loop : -0.08 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 218 HIS 0.003 0.001 HIS G 44 PHE 0.014 0.001 PHE R 165 TYR 0.010 0.001 TYR N 60 ARG 0.010 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 132 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8012 (mptt) REVERT: A 200 LYS cc_start: 0.8937 (mttp) cc_final: 0.8658 (mmtt) REVERT: A 321 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7120 (mtp85) REVERT: A 355 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8249 (t0) REVERT: B 259 GLN cc_start: 0.7750 (tt0) cc_final: 0.7062 (pt0) REVERT: R 51 PHE cc_start: 0.7714 (m-80) cc_final: 0.7431 (m-80) REVERT: R 80 SER cc_start: 0.8166 (t) cc_final: 0.7318 (p) REVERT: R 135 MET cc_start: 0.8753 (mmp) cc_final: 0.8484 (mmt) outliers start: 31 outliers final: 17 residues processed: 156 average time/residue: 1.1826 time to fit residues: 196.5432 Evaluate side-chains 149 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 271 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN R 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8406 Z= 0.199 Angle : 0.475 5.597 11384 Z= 0.256 Chirality : 0.041 0.148 1275 Planarity : 0.004 0.047 1448 Dihedral : 4.895 55.310 1148 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.49 % Allowed : 17.45 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.26), residues: 1031 helix: 1.81 (0.25), residues: 430 sheet: 0.41 (0.34), residues: 223 loop : -0.06 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 218 HIS 0.003 0.001 HIS R 63 PHE 0.013 0.001 PHE A 196 TYR 0.013 0.001 TYR R 27 ARG 0.011 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7983 (mptt) REVERT: A 200 LYS cc_start: 0.8937 (mttp) cc_final: 0.8660 (mmtt) REVERT: A 213 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7702 (p0) REVERT: A 288 GLU cc_start: 0.7825 (mp0) cc_final: 0.7625 (mp0) REVERT: A 321 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7126 (mtp85) REVERT: A 355 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8254 (t0) REVERT: B 175 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7961 (mp10) REVERT: B 259 GLN cc_start: 0.7734 (tt0) cc_final: 0.7101 (pt0) REVERT: R 51 PHE cc_start: 0.7721 (m-80) cc_final: 0.7424 (m-80) REVERT: R 80 SER cc_start: 0.8156 (t) cc_final: 0.7302 (p) REVERT: R 135 MET cc_start: 0.8735 (mmp) cc_final: 0.8463 (mmt) outliers start: 31 outliers final: 21 residues processed: 161 average time/residue: 1.1528 time to fit residues: 198.1054 Evaluate side-chains 155 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 271 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.0040 chunk 61 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8406 Z= 0.205 Angle : 0.485 6.263 11384 Z= 0.261 Chirality : 0.041 0.148 1275 Planarity : 0.004 0.049 1448 Dihedral : 4.871 55.348 1148 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.49 % Allowed : 17.34 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.26), residues: 1031 helix: 1.82 (0.25), residues: 430 sheet: 0.39 (0.34), residues: 223 loop : -0.10 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 218 HIS 0.003 0.001 HIS A 331 PHE 0.013 0.001 PHE A 196 TYR 0.014 0.001 TYR R 279 ARG 0.010 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7711 (tmtt) REVERT: A 200 LYS cc_start: 0.8938 (mttp) cc_final: 0.8663 (mmtt) REVERT: A 213 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7659 (p0) REVERT: A 321 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7126 (mtp85) REVERT: A 355 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8251 (t0) REVERT: B 259 GLN cc_start: 0.7738 (tt0) cc_final: 0.7125 (pt0) REVERT: B 262 MET cc_start: 0.8706 (tpp) cc_final: 0.8503 (ttm) REVERT: R 51 PHE cc_start: 0.7732 (m-80) cc_final: 0.7431 (m-80) REVERT: R 80 SER cc_start: 0.8150 (t) cc_final: 0.6935 (p) REVERT: R 83 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.5095 (ttm170) REVERT: R 135 MET cc_start: 0.8736 (mmp) cc_final: 0.8464 (mmt) outliers start: 31 outliers final: 21 residues processed: 151 average time/residue: 1.2318 time to fit residues: 199.2225 Evaluate side-chains 153 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 127 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 271 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8406 Z= 0.173 Angle : 0.468 5.771 11384 Z= 0.252 Chirality : 0.041 0.209 1275 Planarity : 0.004 0.049 1448 Dihedral : 4.593 55.168 1148 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.70 % Allowed : 18.58 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.26), residues: 1031 helix: 1.89 (0.26), residues: 430 sheet: 0.49 (0.34), residues: 222 loop : -0.14 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 218 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE A 196 TYR 0.012 0.001 TYR R 279 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 139 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7716 (tmtt) REVERT: A 200 LYS cc_start: 0.8926 (mttp) cc_final: 0.8658 (mmtt) REVERT: A 213 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7654 (p0) REVERT: A 288 GLU cc_start: 0.7847 (mp0) cc_final: 0.7641 (mp0) REVERT: A 321 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7114 (mtp85) REVERT: A 355 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8268 (t0) REVERT: B 259 GLN cc_start: 0.7637 (tt0) cc_final: 0.7095 (pt0) REVERT: R 51 PHE cc_start: 0.7711 (m-80) cc_final: 0.7403 (m-80) REVERT: R 80 SER cc_start: 0.8104 (t) cc_final: 0.7260 (p) outliers start: 24 outliers final: 12 residues processed: 159 average time/residue: 1.2085 time to fit residues: 204.3380 Evaluate side-chains 148 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8406 Z= 0.267 Angle : 0.516 6.701 11384 Z= 0.277 Chirality : 0.043 0.184 1275 Planarity : 0.004 0.050 1448 Dihedral : 4.720 54.588 1146 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.70 % Allowed : 18.92 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.26), residues: 1031 helix: 1.77 (0.25), residues: 430 sheet: 0.26 (0.33), residues: 225 loop : -0.13 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 218 HIS 0.004 0.001 HIS R 63 PHE 0.015 0.001 PHE R 70 TYR 0.014 0.001 TYR R 279 ARG 0.013 0.000 ARG A 330 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7698 (tmtt) REVERT: A 200 LYS cc_start: 0.8941 (mttp) cc_final: 0.8659 (mmtt) REVERT: A 213 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7662 (p0) REVERT: A 321 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7140 (mtp85) REVERT: A 330 ARG cc_start: 0.7889 (mtm110) cc_final: 0.7642 (mtm110) REVERT: A 355 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8261 (t0) REVERT: B 19 ARG cc_start: 0.7101 (ttm110) cc_final: 0.6775 (ttm110) REVERT: B 259 GLN cc_start: 0.7775 (tt0) cc_final: 0.7253 (pt0) REVERT: R 51 PHE cc_start: 0.7702 (m-80) cc_final: 0.7397 (m-80) REVERT: R 80 SER cc_start: 0.8229 (t) cc_final: 0.7002 (p) REVERT: R 83 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.5111 (ttm170) outliers start: 24 outliers final: 14 residues processed: 146 average time/residue: 1.1938 time to fit residues: 185.3414 Evaluate side-chains 146 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.150443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.105268 restraints weight = 9285.016| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.32 r_work: 0.3134 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 8406 Z= 0.192 Angle : 0.480 6.254 11384 Z= 0.260 Chirality : 0.041 0.178 1275 Planarity : 0.004 0.052 1448 Dihedral : 4.595 54.200 1146 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.36 % Allowed : 19.71 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1031 helix: 1.80 (0.25), residues: 430 sheet: 0.34 (0.33), residues: 222 loop : -0.16 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 218 HIS 0.003 0.001 HIS B 91 PHE 0.015 0.001 PHE R 154 TYR 0.016 0.001 TYR N 60 ARG 0.013 0.000 ARG A 330 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3607.14 seconds wall clock time: 64 minutes 45.22 seconds (3885.22 seconds total)