Starting phenix.real_space_refine on Sat Apr 6 13:48:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgf_36232/04_2024/8jgf_36232_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgf_36232/04_2024/8jgf_36232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgf_36232/04_2024/8jgf_36232.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgf_36232/04_2024/8jgf_36232.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgf_36232/04_2024/8jgf_36232_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgf_36232/04_2024/8jgf_36232_neut.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.035 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 52 5.16 5 C 5323 2.51 5 N 1412 2.21 5 O 1551 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 GLU 20": "OE1" <-> "OE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "R GLU 119": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8338 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1839 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2477 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 2, 'ARG:plan': 8, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 81 Chain: "E" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1742 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 384 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "L" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 110 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 10} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1786 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 49 Time building chain proxies: 4.87, per 1000 atoms: 0.58 Number of scatterers: 8338 At special positions: 0 Unit cell: (94.64, 119.6, 112.32, 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 52 16.00 O 1551 8.00 N 1412 7.00 C 5323 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 95 " 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: 3.31 Conformation dependent library (CDL) restraints added in 1.8 seconds 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 37.9% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.823A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.874A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 246 through 250 removed outlier: 3.939A pdb=" N ARG A 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.781A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 11 through 31 Processing helix chain 'B' and resid 34 through 40 Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 28 through 44 Processing helix chain 'R' and resid 26 through 28 No H-bonds generated for 'chain 'R' and resid 26 through 28' Processing helix chain 'R' and resid 29 through 55 removed outlier: 3.796A pdb=" N CYS R 35 " --> pdb=" O THR R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 85 removed outlier: 3.962A pdb=" N ASN R 67 " --> pdb=" O ILE R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 126 Processing helix chain 'R' and resid 126 through 133 Processing helix chain 'R' and resid 137 through 160 Processing helix chain 'R' and resid 175 through 205 Processing helix chain 'R' and resid 211 through 228 Processing helix chain 'R' and resid 229 through 239 removed outlier: 4.459A pdb=" N GLY R 233 " --> pdb=" O GLY R 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 252 Processing helix chain 'R' and resid 254 through 273 Proline residue: R 269 - end of helix Processing helix chain 'R' and resid 273 through 278 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 9.092A pdb=" N ALA A 220 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 5.482A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.534A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 4.004A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 139 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 158 removed outlier: 6.074A pdb=" N GLN B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 3.653A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.527A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.635A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 5.888A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ARG E 37 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N TRP E 46 " --> pdb=" O ARG E 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 removed outlier: 5.888A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.951A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1275 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: 2.61 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1409 1.31 - 1.44: 2371 1.44 - 1.56: 4663 1.56 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 8515 Sorted by residual: bond pdb=" CA PHE B 240 " pdb=" C PHE B 240 " ideal model delta sigma weight residual 1.523 1.430 0.092 1.28e-02 6.10e+03 5.22e+01 bond pdb=" CA LYS L 19 " pdb=" C LYS L 19 " ideal model delta sigma weight residual 1.524 1.427 0.096 1.35e-02 5.49e+03 5.09e+01 bond pdb=" CA SER R 176 " pdb=" C SER R 176 " ideal model delta sigma weight residual 1.524 1.440 0.083 1.32e-02 5.74e+03 3.99e+01 bond pdb=" CA TRP R 50 " pdb=" C TRP R 50 " ideal model delta sigma weight residual 1.524 1.454 0.071 1.24e-02 6.50e+03 3.24e+01 bond pdb=" CA VAL R 48 " pdb=" C VAL R 48 " ideal model delta sigma weight residual 1.524 1.451 0.072 1.30e-02 5.92e+03 3.10e+01 ... (remaining 8510 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.68: 227 106.68 - 113.51: 4677 113.51 - 120.35: 3123 120.35 - 127.19: 3465 127.19 - 134.03: 99 Bond angle restraints: 11591 Sorted by residual: angle pdb=" N TYR R 64 " pdb=" CA TYR R 64 " pdb=" C TYR R 64 " ideal model delta sigma weight residual 114.04 100.69 13.35 1.24e+00 6.50e-01 1.16e+02 angle pdb=" N ILE R 63 " pdb=" CA ILE R 63 " pdb=" C ILE R 63 " ideal model delta sigma weight residual 112.83 102.73 10.10 9.90e-01 1.02e+00 1.04e+02 angle pdb=" C GLY A 45 " pdb=" N LYS A 46 " pdb=" CA LYS A 46 " ideal model delta sigma weight residual 120.38 132.21 -11.83 1.37e+00 5.33e-01 7.46e+01 angle pdb=" N LEU B 157 " pdb=" CA LEU B 157 " pdb=" C LEU B 157 " ideal model delta sigma weight residual 113.97 103.28 10.69 1.28e+00 6.10e-01 6.97e+01 angle pdb=" N THR R 175 " pdb=" CA THR R 175 " pdb=" C THR R 175 " ideal model delta sigma weight residual 113.30 102.75 10.55 1.34e+00 5.57e-01 6.20e+01 ... (remaining 11586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4438 17.84 - 35.68: 420 35.68 - 53.52: 97 53.52 - 71.36: 20 71.36 - 89.21: 11 Dihedral angle restraints: 4986 sinusoidal: 1794 harmonic: 3192 Sorted by residual: dihedral pdb=" C MET L 15 " pdb=" N MET L 15 " pdb=" CA MET L 15 " pdb=" CB MET L 15 " ideal model delta harmonic sigma weight residual -122.60 -108.45 -14.15 0 2.50e+00 1.60e-01 3.21e+01 dihedral pdb=" CA PHE E 31 " pdb=" C PHE E 31 " pdb=" N GLY E 32 " pdb=" CA GLY E 32 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C PHE B 240 " pdb=" N PHE B 240 " pdb=" CA PHE B 240 " pdb=" CB PHE B 240 " ideal model delta harmonic sigma weight residual -122.60 -112.58 -10.02 0 2.50e+00 1.60e-01 1.61e+01 ... (remaining 4983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1076 0.052 - 0.104: 208 0.104 - 0.156: 51 0.156 - 0.207: 6 0.207 - 0.259: 5 Chirality restraints: 1346 Sorted by residual: chirality pdb=" CA ARG E 191 " pdb=" N ARG E 191 " pdb=" C ARG E 191 " pdb=" CB ARG E 191 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA LYS B 83 " pdb=" N LYS B 83 " pdb=" C LYS B 83 " pdb=" CB LYS B 83 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA MET L 15 " pdb=" N MET L 15 " pdb=" C MET L 15 " pdb=" CB MET L 15 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1343 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU R 157 " -0.018 2.00e-02 2.50e+03 3.54e-02 1.26e+01 pdb=" C GLU R 157 " 0.061 2.00e-02 2.50e+03 pdb=" O GLU R 157 " -0.023 2.00e-02 2.50e+03 pdb=" N TRP R 158 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 240 " 0.055 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO B 241 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO B 241 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 241 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 45 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.37e+00 pdb=" C ASN R 45 " -0.053 2.00e-02 2.50e+03 pdb=" O ASN R 45 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA R 46 " 0.018 2.00e-02 2.50e+03 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1497 2.76 - 3.29: 8373 3.29 - 3.83: 14942 3.83 - 4.36: 18121 4.36 - 4.90: 30263 Nonbonded interactions: 73196 Sorted by model distance: nonbonded pdb=" O ILE B 63 " pdb=" OG SER B 321 " model vdw 2.221 2.440 nonbonded pdb=" OG SER B 152 " pdb=" O VAL B 192 " model vdw 2.242 2.440 nonbonded pdb=" OE2 GLU B 265 " pdb=" OG1 THR B 268 " model vdw 2.275 2.440 nonbonded pdb=" O THR B 91 " pdb=" OG1 THR B 92 " model vdw 2.281 2.440 nonbonded pdb=" O HIS B 59 " pdb=" OG SER B 339 " model vdw 2.285 2.440 ... (remaining 73191 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 2.160 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.720 Find NCS groups from input model: 0.270 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:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 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 : 0.008 0.096 8515 Z= 0.502 Angle : 0.860 13.354 11591 Z= 0.565 Chirality : 0.047 0.259 1346 Planarity : 0.005 0.081 1468 Dihedral : 15.546 89.206 2919 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.58 % Allowed : 20.21 % Favored : 79.21 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.26), residues: 1081 helix: 1.25 (0.28), residues: 362 sheet: -0.50 (0.29), residues: 281 loop : -0.22 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 158 HIS 0.007 0.001 HIS B 147 PHE 0.024 0.002 PHE B 240 TYR 0.028 0.002 TYR R 64 ARG 0.004 0.001 ARG E 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 287 time to evaluate : 0.924 Fit side-chains REVERT: A 49 ILE cc_start: 0.7450 (mt) cc_final: 0.7078 (OUTLIER) REVERT: B 25 ASP cc_start: 0.6993 (m-30) cc_final: 0.6791 (m-30) REVERT: B 258 PHE cc_start: 0.8034 (m-80) cc_final: 0.7740 (m-80) REVERT: B 263 ASP cc_start: 0.7212 (t70) cc_final: 0.6962 (t0) REVERT: R 80 LEU cc_start: 0.7865 (tp) cc_final: 0.7507 (tt) outliers start: 5 outliers final: 2 residues processed: 289 average time/residue: 1.1405 time to fit residues: 351.3768 Evaluate side-chains 227 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 226 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.2980 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 261 GLN B 37 GLN B 93 ASN B 137 ASN B 180 GLN B 264 GLN B 345 ASN G 58 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8515 Z= 0.196 Angle : 0.548 7.215 11591 Z= 0.289 Chirality : 0.042 0.155 1346 Planarity : 0.004 0.056 1468 Dihedral : 4.308 21.459 1179 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 5.81 % Allowed : 22.76 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.26), residues: 1081 helix: 2.04 (0.27), residues: 370 sheet: -0.17 (0.30), residues: 274 loop : 0.03 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 174 HIS 0.002 0.001 HIS R 133 PHE 0.021 0.002 PHE E 28 TYR 0.027 0.001 TYR L 17 ARG 0.007 0.001 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 253 time to evaluate : 0.859 Fit side-chains REVERT: B 10 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.4664 (t0) REVERT: B 11 GLN cc_start: 0.5697 (mm110) cc_final: 0.5049 (mm110) REVERT: B 19 LEU cc_start: 0.8545 (mm) cc_final: 0.8021 (mm) REVERT: B 32 ASP cc_start: 0.7868 (p0) cc_final: 0.7625 (p0) REVERT: B 79 SER cc_start: 0.6995 (OUTLIER) cc_final: 0.6717 (p) REVERT: B 142 ARG cc_start: 0.7191 (ttm110) cc_final: 0.6968 (ttp-170) REVERT: B 258 PHE cc_start: 0.8016 (m-80) cc_final: 0.7713 (m-80) REVERT: B 263 ASP cc_start: 0.7165 (t70) cc_final: 0.6774 (t0) REVERT: B 345 ASN cc_start: 0.6710 (OUTLIER) cc_final: 0.6488 (t0) REVERT: E 202 ARG cc_start: 0.7786 (mtp180) cc_final: 0.7522 (mtp180) REVERT: R 101 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.8137 (p) REVERT: R 152 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8251 (tp) REVERT: R 198 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7279 (tp) outliers start: 50 outliers final: 18 residues processed: 281 average time/residue: 1.0219 time to fit residues: 308.8970 Evaluate side-chains 266 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 242 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 258 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN A 354 ASN B 21 ASN B 37 GLN B 264 GLN B 345 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8515 Z= 0.199 Angle : 0.536 8.661 11591 Z= 0.279 Chirality : 0.041 0.168 1346 Planarity : 0.004 0.055 1468 Dihedral : 4.103 20.511 1177 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.30 % Allowed : 27.18 % Favored : 68.52 % 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: 1.33 (0.26), residues: 1081 helix: 2.57 (0.26), residues: 365 sheet: 0.11 (0.30), residues: 269 loop : 0.02 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 211 HIS 0.003 0.001 HIS B 147 PHE 0.024 0.002 PHE E 28 TYR 0.034 0.001 TYR L 17 ARG 0.006 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 261 time to evaluate : 0.961 Fit side-chains REVERT: A 340 ARG cc_start: 0.7589 (tpp-160) cc_final: 0.7316 (tpt170) REVERT: B 10 ASP cc_start: 0.7034 (OUTLIER) cc_final: 0.4364 (t0) REVERT: B 66 MET cc_start: 0.6490 (ppp) cc_final: 0.6160 (ttp) REVERT: B 258 PHE cc_start: 0.8047 (m-80) cc_final: 0.7751 (m-80) REVERT: B 263 ASP cc_start: 0.7079 (t70) cc_final: 0.6728 (t0) REVERT: E 203 PHE cc_start: 0.8405 (m-80) cc_final: 0.7844 (m-80) REVERT: R 36 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7857 (mp) REVERT: R 101 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.8117 (p) REVERT: R 152 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8220 (tp) outliers start: 37 outliers final: 19 residues processed: 281 average time/residue: 0.9800 time to fit residues: 296.1749 Evaluate side-chains 267 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 244 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 258 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 338 ASN B 225 GLN B 264 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN E 142 GLN E 194 ASN ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8515 Z= 0.192 Angle : 0.519 7.646 11591 Z= 0.269 Chirality : 0.041 0.159 1346 Planarity : 0.004 0.048 1468 Dihedral : 4.007 20.049 1177 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.88 % Allowed : 28.80 % Favored : 66.32 % 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: 1.47 (0.26), residues: 1081 helix: 2.77 (0.25), residues: 366 sheet: 0.18 (0.31), residues: 277 loop : 0.02 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 211 HIS 0.003 0.001 HIS B 147 PHE 0.027 0.002 PHE E 28 TYR 0.032 0.001 TYR L 17 ARG 0.008 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 250 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 340 ARG cc_start: 0.7573 (tpp-160) cc_final: 0.7289 (tpt170) REVERT: B 10 ASP cc_start: 0.7194 (OUTLIER) cc_final: 0.4647 (t0) REVERT: B 18 GLN cc_start: 0.7728 (tm-30) cc_final: 0.7465 (tm-30) REVERT: B 258 PHE cc_start: 0.8023 (m-80) cc_final: 0.7749 (m-80) REVERT: B 263 ASP cc_start: 0.7062 (t70) cc_final: 0.6758 (t0) REVERT: E 203 PHE cc_start: 0.8401 (m-80) cc_final: 0.7855 (m-80) REVERT: R 36 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7885 (mp) REVERT: R 152 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8202 (tp) outliers start: 42 outliers final: 24 residues processed: 271 average time/residue: 0.9901 time to fit residues: 288.8985 Evaluate side-chains 273 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 246 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 102 MET Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 258 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 26 optimal weight: 0.0870 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 338 ASN A 354 ASN B 11 GLN B 225 GLN B 264 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8515 Z= 0.159 Angle : 0.516 7.135 11591 Z= 0.265 Chirality : 0.041 0.163 1346 Planarity : 0.004 0.044 1468 Dihedral : 3.873 19.445 1177 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.18 % Allowed : 29.27 % Favored : 66.55 % 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: 1.48 (0.26), residues: 1081 helix: 2.81 (0.25), residues: 370 sheet: 0.26 (0.31), residues: 277 loop : -0.09 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 174 HIS 0.002 0.001 HIS E 34 PHE 0.028 0.001 PHE E 28 TYR 0.030 0.001 TYR L 17 ARG 0.008 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 257 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 298 ASP cc_start: 0.7151 (t0) cc_final: 0.6819 (t0) REVERT: A 337 GLU cc_start: 0.6530 (mp0) cc_final: 0.6213 (mp0) REVERT: A 340 ARG cc_start: 0.7519 (tpp-160) cc_final: 0.7251 (tpt170) REVERT: B 10 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.4754 (t70) REVERT: B 258 PHE cc_start: 0.8029 (m-80) cc_final: 0.7797 (m-80) REVERT: B 263 ASP cc_start: 0.7015 (t70) cc_final: 0.6741 (t0) REVERT: E 203 PHE cc_start: 0.8387 (m-80) cc_final: 0.7839 (m-80) REVERT: R 36 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7873 (mp) REVERT: R 152 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8160 (tp) outliers start: 36 outliers final: 20 residues processed: 276 average time/residue: 0.9760 time to fit residues: 290.6119 Evaluate side-chains 260 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 237 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 102 MET Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 258 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 86 optimal weight: 0.0570 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 338 ASN A 354 ASN B 11 GLN B 225 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8515 Z= 0.167 Angle : 0.526 6.971 11591 Z= 0.268 Chirality : 0.041 0.158 1346 Planarity : 0.004 0.043 1468 Dihedral : 3.871 19.171 1177 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.53 % Allowed : 30.31 % Favored : 65.16 % 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: 1.48 (0.26), residues: 1081 helix: 2.90 (0.25), residues: 370 sheet: 0.23 (0.32), residues: 279 loop : -0.16 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 174 HIS 0.003 0.001 HIS B 230 PHE 0.030 0.001 PHE E 28 TYR 0.028 0.001 TYR L 17 ARG 0.008 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 242 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 340 ARG cc_start: 0.7540 (tpp-160) cc_final: 0.7232 (tpt170) REVERT: B 10 ASP cc_start: 0.7086 (OUTLIER) cc_final: 0.4676 (t70) REVERT: B 263 ASP cc_start: 0.6971 (t70) cc_final: 0.6667 (t0) REVERT: E 203 PHE cc_start: 0.8394 (m-80) cc_final: 0.7844 (m-80) REVERT: R 36 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7839 (mp) REVERT: R 152 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8145 (tp) outliers start: 39 outliers final: 22 residues processed: 259 average time/residue: 1.1054 time to fit residues: 306.3116 Evaluate side-chains 256 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 231 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 83 SER Chi-restraints excluded: chain R residue 102 MET Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 258 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 338 ASN B 11 GLN B 225 GLN B 264 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8515 Z= 0.208 Angle : 0.556 10.966 11591 Z= 0.280 Chirality : 0.042 0.163 1346 Planarity : 0.004 0.043 1468 Dihedral : 3.929 19.020 1177 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.88 % Allowed : 30.89 % Favored : 64.23 % 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: 1.39 (0.26), residues: 1081 helix: 2.91 (0.25), residues: 366 sheet: 0.29 (0.32), residues: 277 loop : -0.35 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 211 HIS 0.003 0.001 HIS B 147 PHE 0.031 0.002 PHE E 28 TYR 0.027 0.001 TYR L 17 ARG 0.008 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 235 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 192 ASP cc_start: 0.6179 (m-30) cc_final: 0.5573 (m-30) REVERT: A 340 ARG cc_start: 0.7666 (tpp-160) cc_final: 0.7369 (tpt170) REVERT: B 10 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.4492 (t70) REVERT: B 263 ASP cc_start: 0.6997 (t70) cc_final: 0.6673 (t0) REVERT: E 203 PHE cc_start: 0.8408 (m-80) cc_final: 0.7877 (m-80) REVERT: R 36 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7836 (mp) REVERT: R 103 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.6635 (mpt) REVERT: R 152 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8149 (tp) outliers start: 42 outliers final: 25 residues processed: 254 average time/residue: 1.0577 time to fit residues: 289.1180 Evaluate side-chains 263 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 234 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 83 SER Chi-restraints excluded: chain R residue 102 MET Chi-restraints excluded: chain R residue 103 MET Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 258 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 261 GLN A 338 ASN B 11 GLN B 225 GLN B 264 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8515 Z= 0.255 Angle : 0.581 10.024 11591 Z= 0.293 Chirality : 0.043 0.163 1346 Planarity : 0.004 0.043 1468 Dihedral : 4.074 19.105 1177 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.18 % Allowed : 31.13 % Favored : 64.69 % 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: 1.31 (0.26), residues: 1081 helix: 2.83 (0.25), residues: 366 sheet: 0.22 (0.32), residues: 283 loop : -0.37 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 211 HIS 0.003 0.001 HIS B 147 PHE 0.033 0.002 PHE E 28 TYR 0.026 0.002 TYR L 17 ARG 0.009 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 241 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 192 ASP cc_start: 0.6203 (m-30) cc_final: 0.5626 (m-30) REVERT: A 340 ARG cc_start: 0.7718 (tpp-160) cc_final: 0.7397 (tpt170) REVERT: B 10 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.4504 (t70) REVERT: B 258 PHE cc_start: 0.8079 (m-80) cc_final: 0.7793 (m-80) REVERT: B 263 ASP cc_start: 0.7064 (t70) cc_final: 0.6737 (t0) REVERT: E 203 PHE cc_start: 0.8415 (m-80) cc_final: 0.7878 (m-80) REVERT: R 36 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7886 (mp) REVERT: R 103 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.6667 (mpt) REVERT: R 152 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8165 (tp) outliers start: 36 outliers final: 25 residues processed: 257 average time/residue: 1.0024 time to fit residues: 277.4461 Evaluate side-chains 266 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 237 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 33 MET Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 102 MET Chi-restraints excluded: chain R residue 103 MET Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 258 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 261 GLN A 338 ASN B 11 GLN B 225 GLN B 264 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8515 Z= 0.215 Angle : 0.566 9.012 11591 Z= 0.287 Chirality : 0.043 0.227 1346 Planarity : 0.004 0.042 1468 Dihedral : 4.029 18.803 1177 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.83 % Allowed : 31.13 % Favored : 65.04 % 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: 1.32 (0.26), residues: 1081 helix: 2.79 (0.25), residues: 367 sheet: 0.32 (0.32), residues: 277 loop : -0.41 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 211 HIS 0.002 0.001 HIS B 147 PHE 0.033 0.002 PHE E 28 TYR 0.022 0.001 TYR L 17 ARG 0.009 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 236 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 192 ASP cc_start: 0.6169 (m-30) cc_final: 0.5551 (m-30) REVERT: A 298 ASP cc_start: 0.7332 (t0) cc_final: 0.6924 (t0) REVERT: A 340 ARG cc_start: 0.7660 (tpp-160) cc_final: 0.7331 (tpt170) REVERT: B 10 ASP cc_start: 0.7239 (OUTLIER) cc_final: 0.4431 (t70) REVERT: B 263 ASP cc_start: 0.7041 (t70) cc_final: 0.6719 (t0) REVERT: R 36 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7870 (mp) REVERT: R 152 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8150 (tp) outliers start: 33 outliers final: 21 residues processed: 252 average time/residue: 1.0367 time to fit residues: 280.3846 Evaluate side-chains 255 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 231 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 102 MET Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain R residue 180 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 8 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 68 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: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 261 GLN B 11 GLN B 225 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8515 Z= 0.218 Angle : 0.590 11.047 11591 Z= 0.294 Chirality : 0.044 0.226 1346 Planarity : 0.004 0.042 1468 Dihedral : 4.033 18.596 1177 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.72 % Allowed : 31.48 % Favored : 64.81 % 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: 1.33 (0.26), residues: 1081 helix: 2.79 (0.25), residues: 367 sheet: 0.36 (0.32), residues: 277 loop : -0.41 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 211 HIS 0.002 0.001 HIS B 147 PHE 0.034 0.002 PHE E 28 TYR 0.029 0.001 TYR L 17 ARG 0.009 0.001 ARG B 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 232 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 192 ASP cc_start: 0.6169 (m-30) cc_final: 0.5540 (m-30) REVERT: A 340 ARG cc_start: 0.7659 (tpp-160) cc_final: 0.7321 (tpt170) REVERT: B 10 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.4381 (t70) REVERT: B 263 ASP cc_start: 0.7012 (t70) cc_final: 0.6706 (t0) REVERT: E 203 PHE cc_start: 0.8410 (m-80) cc_final: 0.7886 (m-80) REVERT: R 36 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7873 (mp) REVERT: R 152 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8140 (tp) outliers start: 32 outliers final: 26 residues processed: 248 average time/residue: 1.0276 time to fit residues: 274.0125 Evaluate side-chains 259 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 230 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 83 SER Chi-restraints excluded: chain R residue 102 MET Chi-restraints excluded: chain R residue 119 GLU Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain R residue 180 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 35 optimal weight: 0.0030 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 261 GLN B 11 GLN B 225 GLN B 264 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.118334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.109096 restraints weight = 12383.821| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.79 r_work: 0.3486 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8515 Z= 0.198 Angle : 0.570 8.753 11591 Z= 0.287 Chirality : 0.043 0.209 1346 Planarity : 0.004 0.043 1468 Dihedral : 4.001 18.346 1177 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.72 % Allowed : 31.36 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.26), residues: 1081 helix: 2.80 (0.25), residues: 367 sheet: 0.37 (0.32), residues: 277 loop : -0.39 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 174 HIS 0.002 0.001 HIS B 147 PHE 0.035 0.002 PHE E 28 TYR 0.030 0.001 TYR L 17 ARG 0.010 0.001 ARG B 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4667.52 seconds wall clock time: 83 minutes 55.54 seconds (5035.54 seconds total)