Starting phenix.real_space_refine on Wed Feb 14 05:34:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihb_35442/02_2024/8ihb_35442_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihb_35442/02_2024/8ihb_35442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihb_35442/02_2024/8ihb_35442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihb_35442/02_2024/8ihb_35442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihb_35442/02_2024/8ihb_35442_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihb_35442/02_2024/8ihb_35442_updated.pdb" } resolution = 2.85 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= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 62 5.16 5 Cl 1 4.86 5 C 5568 2.51 5 N 1480 2.21 5 O 1597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8708 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2385 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 281} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1706 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "S" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1709 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2491 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 85 Chain: "C" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 386 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "R" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'NAG': 1, 'OKL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.04, per 1000 atoms: 0.58 Number of scatterers: 8708 At special positions: 0 Unit cell: (86.32, 116.2, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 62 16.00 O 1597 8.00 N 1480 7.00 C 5568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 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 Links applied NAG-ASN " NAG R 601 " - " ASN R 17 " Time building additional restraints: 3.65 Conformation dependent library (CDL) restraints added in 1.9 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 16 sheets defined 33.4% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'R' and resid 24 through 27 No H-bonds generated for 'chain 'R' and resid 24 through 27' Processing helix chain 'R' and resid 30 through 54 Processing helix chain 'R' and resid 61 through 77 Processing helix chain 'R' and resid 80 through 87 Processing helix chain 'R' and resid 98 through 129 removed outlier: 3.537A pdb=" N LEU R 104 " --> pdb=" O CYS R 100 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN R 110 " --> pdb=" O MET R 106 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL R 121 " --> pdb=" O PHE R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 138 Processing helix chain 'R' and resid 141 through 157 Processing helix chain 'R' and resid 160 through 164 Processing helix chain 'R' and resid 188 through 195 Processing helix chain 'R' and resid 198 through 217 removed outlier: 3.560A pdb=" N ILE R 203 " --> pdb=" O LEU R 199 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 260 removed outlier: 3.527A pdb=" N THR R 231 " --> pdb=" O LYS R 227 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 270 through 282 removed outlier: 3.595A pdb=" N LEU R 274 " --> pdb=" O ARG R 270 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE R 277 " --> pdb=" O ASP R 273 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 285 through 294 Proline residue: R 291 - end of helix Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.580A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.153A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.713A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.682A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing sheet with id= A, first strand: chain 'R' and resid 11 through 13 Processing sheet with id= B, first strand: chain 'R' and resid 169 through 171 Processing sheet with id= C, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.494A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'S' and resid 18 through 23 Processing sheet with id= E, first strand: chain 'S' and resid 33 through 35 Processing sheet with id= F, first strand: chain 'S' and resid 38 through 40 Processing sheet with id= G, first strand: chain 'S' and resid 49 through 51 Processing sheet with id= H, first strand: chain 'S' and resid 156 through 160 Processing sheet with id= I, first strand: chain 'S' and resid 226 through 231 removed outlier: 3.522A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.783A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.828A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.776A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 198 through 202 removed outlier: 3.514A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.468A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.472A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.508A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 1023 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: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1902 1.33 - 1.46: 2600 1.46 - 1.58: 4313 1.58 - 1.71: 1 1.71 - 1.84: 88 Bond restraints: 8904 Sorted by residual: bond pdb=" C SER B 331 " pdb=" O SER B 331 " ideal model delta sigma weight residual 1.233 1.201 0.032 1.17e-02 7.31e+03 7.55e+00 bond pdb=" CA SER B 316 " pdb=" C SER B 316 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.37e-02 5.33e+03 7.18e+00 bond pdb=" C15 OKL R 602 " pdb=" N16 OKL R 602 " ideal model delta sigma weight residual 1.335 1.383 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" C SER B 316 " pdb=" O SER B 316 " ideal model delta sigma weight residual 1.236 1.207 0.029 1.29e-02 6.01e+03 4.97e+00 bond pdb=" CA SER B 316 " pdb=" CB SER B 316 " ideal model delta sigma weight residual 1.529 1.494 0.036 1.63e-02 3.76e+03 4.76e+00 ... (remaining 8899 not shown) Histogram of bond angle deviations from ideal: 97.34 - 104.67: 103 104.67 - 112.01: 4437 112.01 - 119.34: 2898 119.34 - 126.68: 4501 126.68 - 134.01: 145 Bond angle restraints: 12084 Sorted by residual: angle pdb=" N SER B 316 " pdb=" CA SER B 316 " pdb=" C SER B 316 " ideal model delta sigma weight residual 112.23 117.57 -5.34 1.26e+00 6.30e-01 1.80e+01 angle pdb=" N SER B 316 " pdb=" CA SER B 316 " pdb=" CB SER B 316 " ideal model delta sigma weight residual 110.30 105.45 4.85 1.54e+00 4.22e-01 9.92e+00 angle pdb=" N SER B 331 " pdb=" CA SER B 331 " pdb=" C SER B 331 " ideal model delta sigma weight residual 108.60 113.17 -4.57 1.46e+00 4.69e-01 9.80e+00 angle pdb=" C ASP R 97 " pdb=" N ILE R 98 " pdb=" CA ILE R 98 " ideal model delta sigma weight residual 120.33 122.57 -2.24 8.00e-01 1.56e+00 7.81e+00 angle pdb=" CA TYR S 235 " pdb=" CB TYR S 235 " pdb=" CG TYR S 235 " ideal model delta sigma weight residual 113.90 109.47 4.43 1.80e+00 3.09e-01 6.06e+00 ... (remaining 12079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.42: 4733 23.42 - 46.85: 430 46.85 - 70.27: 56 70.27 - 93.69: 7 93.69 - 117.11: 1 Dihedral angle restraints: 5227 sinusoidal: 1951 harmonic: 3276 Sorted by residual: dihedral pdb=" CA PHE R 117 " pdb=" C PHE R 117 " pdb=" N LEU R 118 " pdb=" CA LEU R 118 " ideal model delta harmonic sigma weight residual 180.00 155.45 24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CB CYS R 100 " pdb=" SG CYS R 100 " pdb=" SG CYS R 177 " pdb=" CB CYS R 177 " ideal model delta sinusoidal sigma weight residual -86.00 -127.37 41.37 1 1.00e+01 1.00e-02 2.40e+01 dihedral pdb=" CA GLU S 234 " pdb=" C GLU S 234 " pdb=" N TYR S 235 " pdb=" CA TYR S 235 " ideal model delta harmonic sigma weight residual -180.00 -155.77 -24.23 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 5224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 800 0.029 - 0.058: 370 0.058 - 0.087: 119 0.087 - 0.116: 69 0.116 - 0.145: 19 Chirality restraints: 1377 Sorted by residual: chirality pdb=" CA ASP S 90 " pdb=" N ASP S 90 " pdb=" C ASP S 90 " pdb=" CB ASP S 90 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA GLU S 42 " pdb=" N GLU S 42 " pdb=" C GLU S 42 " pdb=" CB GLU S 42 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 1374 not shown) Planarity restraints: 1525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C05 OKL R 602 " -0.012 2.00e-02 2.50e+03 4.05e-02 5.34e+01 pdb=" C07 OKL R 602 " -0.020 2.00e-02 2.50e+03 pdb=" C10 OKL R 602 " 0.006 2.00e-02 2.50e+03 pdb=" C12 OKL R 602 " 0.040 2.00e-02 2.50e+03 pdb=" C13 OKL R 602 " 0.052 2.00e-02 2.50e+03 pdb=" C15 OKL R 602 " 0.019 2.00e-02 2.50e+03 pdb=" N06 OKL R 602 " 0.018 2.00e-02 2.50e+03 pdb=" N09 OKL R 602 " -0.020 2.00e-02 2.50e+03 pdb=" N14 OKL R 602 " 0.052 2.00e-02 2.50e+03 pdb=" N16 OKL R 602 " 0.023 2.00e-02 2.50e+03 pdb=" O08 OKL R 602 " -0.040 2.00e-02 2.50e+03 pdb=" O11 OKL R 602 " -0.016 2.00e-02 2.50e+03 pdb="CL17 OKL R 602 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 235 " 0.029 2.00e-02 2.50e+03 1.74e-02 6.04e+00 pdb=" CG TYR S 235 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR S 235 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR S 235 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR S 235 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR S 235 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR S 235 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR S 235 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO R 31 " 0.035 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO R 32 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO R 32 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 32 " 0.031 5.00e-02 4.00e+02 ... (remaining 1522 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 802 2.74 - 3.28: 8324 3.28 - 3.82: 14402 3.82 - 4.36: 17676 4.36 - 4.90: 31070 Nonbonded interactions: 72274 Sorted by model distance: nonbonded pdb=" NZ LYS A 209 " pdb=" OD2 ASP B 228 " model vdw 2.202 2.520 nonbonded pdb=" O ASP S 223 " pdb=" OH TYR S 227 " model vdw 2.230 2.440 nonbonded pdb=" OD1 ASP B 170 " pdb=" OG1 THR B 173 " model vdw 2.233 2.440 nonbonded pdb=" NH2 ARG B 256 " pdb=" OD2 ASP C 36 " model vdw 2.238 2.520 nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.240 2.520 ... (remaining 72269 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 5.600 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.590 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8904 Z= 0.244 Angle : 0.536 6.950 12084 Z= 0.286 Chirality : 0.042 0.145 1377 Planarity : 0.004 0.054 1524 Dihedral : 17.040 117.112 3100 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.44 % Allowed : 28.24 % Favored : 71.32 % 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: -0.70 (0.24), residues: 1115 helix: -0.01 (0.26), residues: 358 sheet: 0.17 (0.32), residues: 263 loop : -1.08 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.002 0.001 HIS A 188 PHE 0.016 0.001 PHE A 334 TYR 0.039 0.001 TYR S 235 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7931 (mtmm) cc_final: 0.7619 (ptpt) REVERT: R 63 ARG cc_start: 0.8369 (mtp85) cc_final: 0.8168 (mmt90) REVERT: R 170 GLN cc_start: 0.6941 (tm-30) cc_final: 0.6666 (tm130) REVERT: A 263 SER cc_start: 0.8696 (m) cc_final: 0.8295 (p) REVERT: S 83 MET cc_start: 0.9136 (mtm) cc_final: 0.8857 (mtp) REVERT: B 197 ARG cc_start: 0.7465 (mmm160) cc_final: 0.7256 (mmt-90) outliers start: 4 outliers final: 3 residues processed: 144 average time/residue: 1.0995 time to fit residues: 169.6415 Evaluate side-chains 137 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 134 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 183 GLN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8904 Z= 0.327 Angle : 0.590 7.283 12084 Z= 0.314 Chirality : 0.044 0.202 1377 Planarity : 0.004 0.044 1524 Dihedral : 6.357 109.952 1241 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.95 % Allowed : 26.59 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.02 (0.25), residues: 1115 helix: 1.19 (0.27), residues: 357 sheet: 0.24 (0.31), residues: 271 loop : -1.05 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 63 HIS 0.004 0.001 HIS B 91 PHE 0.014 0.002 PHE S 27 TYR 0.033 0.002 TYR S 235 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 133 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7970 (mtmm) cc_final: 0.7461 (ptmt) REVERT: R 101 ARG cc_start: 0.7803 (mtp85) cc_final: 0.7327 (mtt-85) REVERT: R 165 LYS cc_start: 0.7042 (mmmt) cc_final: 0.6817 (mmpt) REVERT: A 15 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.6627 (ttt-90) REVERT: A 209 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7815 (pttp) REVERT: A 276 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: A 281 SER cc_start: 0.7524 (OUTLIER) cc_final: 0.7298 (m) REVERT: A 313 ARG cc_start: 0.5963 (OUTLIER) cc_final: 0.5381 (pmm-80) REVERT: S 42 GLU cc_start: 0.6776 (pp20) cc_final: 0.6516 (pp20) REVERT: S 43 LYS cc_start: 0.8994 (mmmt) cc_final: 0.8523 (mmmt) REVERT: S 77 ASN cc_start: 0.8198 (m-40) cc_final: 0.7936 (m-40) REVERT: S 83 MET cc_start: 0.9242 (mtm) cc_final: 0.8970 (mtp) REVERT: B 195 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7459 (p0) REVERT: B 293 ASN cc_start: 0.8520 (m-40) cc_final: 0.8157 (m-40) outliers start: 45 outliers final: 17 residues processed: 160 average time/residue: 1.1282 time to fit residues: 193.5845 Evaluate side-chains 148 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 0.0050 chunk 99 optimal weight: 0.5980 chunk 34 optimal weight: 0.0470 chunk 80 optimal weight: 0.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 GLN ** S 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8904 Z= 0.141 Angle : 0.488 6.321 12084 Z= 0.259 Chirality : 0.040 0.165 1377 Planarity : 0.003 0.046 1524 Dihedral : 5.640 100.891 1237 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.63 % Allowed : 29.12 % Favored : 67.25 % 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: 0.32 (0.25), residues: 1115 helix: 1.76 (0.27), residues: 362 sheet: 0.34 (0.31), residues: 266 loop : -1.06 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS B 91 PHE 0.015 0.001 PHE A 334 TYR 0.022 0.001 TYR S 235 ARG 0.003 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7895 (mtmm) cc_final: 0.7631 (ptpt) REVERT: R 101 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7174 (mtt-85) REVERT: A 197 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8289 (mttm) REVERT: A 276 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: S 42 GLU cc_start: 0.6744 (pp20) cc_final: 0.6524 (pp20) REVERT: S 43 LYS cc_start: 0.9000 (mmmt) cc_final: 0.8673 (mmmt) REVERT: S 235 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.6692 (t80) REVERT: B 52 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8126 (mtt90) REVERT: B 195 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7480 (p0) REVERT: B 197 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6885 (mtt-85) REVERT: B 293 ASN cc_start: 0.8335 (m-40) cc_final: 0.8000 (m-40) outliers start: 33 outliers final: 14 residues processed: 151 average time/residue: 1.0984 time to fit residues: 177.9157 Evaluate side-chains 146 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 GLN ** S 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8904 Z= 0.199 Angle : 0.514 6.465 12084 Z= 0.272 Chirality : 0.041 0.177 1377 Planarity : 0.004 0.046 1524 Dihedral : 5.444 91.644 1237 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.27 % Allowed : 28.13 % Favored : 66.59 % 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: 0.36 (0.25), residues: 1115 helix: 1.89 (0.27), residues: 362 sheet: 0.26 (0.31), residues: 269 loop : -1.05 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.016 0.001 PHE A 334 TYR 0.022 0.001 TYR S 235 ARG 0.002 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 129 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7929 (mtmm) cc_final: 0.7650 (ptpt) REVERT: R 101 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7228 (mtt-85) REVERT: A 209 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7833 (pttp) REVERT: A 276 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7266 (mp0) REVERT: A 313 ARG cc_start: 0.5995 (OUTLIER) cc_final: 0.5393 (pmm-80) REVERT: S 43 LYS cc_start: 0.8964 (mmmt) cc_final: 0.8539 (mmmt) REVERT: S 235 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.6908 (t80) REVERT: B 52 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8130 (mtt90) REVERT: B 195 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7474 (p0) REVERT: B 197 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6924 (mtt-85) REVERT: B 293 ASN cc_start: 0.8357 (m-40) cc_final: 0.8026 (m-40) outliers start: 48 outliers final: 23 residues processed: 158 average time/residue: 1.0610 time to fit residues: 180.0018 Evaluate side-chains 152 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 0 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8904 Z= 0.208 Angle : 0.530 9.098 12084 Z= 0.276 Chirality : 0.042 0.178 1377 Planarity : 0.003 0.046 1524 Dihedral : 5.372 89.283 1237 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.27 % Allowed : 27.58 % Favored : 67.14 % 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: 0.41 (0.25), residues: 1115 helix: 1.98 (0.27), residues: 362 sheet: 0.26 (0.31), residues: 268 loop : -1.06 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.014 0.001 PHE A 334 TYR 0.023 0.001 TYR S 235 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 129 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7940 (mtmm) cc_final: 0.7657 (ptpt) REVERT: R 101 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7195 (mtt-85) REVERT: A 15 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.6522 (ttt-90) REVERT: A 209 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7817 (pttp) REVERT: A 257 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.7938 (ptmt) REVERT: A 276 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: A 313 ARG cc_start: 0.6023 (OUTLIER) cc_final: 0.5416 (pmm-80) REVERT: S 235 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.6875 (t80) REVERT: B 52 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8117 (mtt90) REVERT: B 195 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7452 (p0) REVERT: B 197 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6922 (mtt-85) REVERT: B 293 ASN cc_start: 0.8356 (m-40) cc_final: 0.8019 (m-40) outliers start: 48 outliers final: 28 residues processed: 158 average time/residue: 1.1302 time to fit residues: 191.2513 Evaluate side-chains 159 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 121 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 55 optimal weight: 0.3980 chunk 102 optimal weight: 6.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8904 Z= 0.156 Angle : 0.501 8.749 12084 Z= 0.261 Chirality : 0.041 0.162 1377 Planarity : 0.003 0.048 1524 Dihedral : 5.155 86.766 1237 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.84 % Allowed : 28.02 % Favored : 67.14 % 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: 0.49 (0.25), residues: 1115 helix: 2.11 (0.27), residues: 362 sheet: 0.24 (0.30), residues: 268 loop : -1.02 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.000 HIS A 188 PHE 0.015 0.001 PHE A 334 TYR 0.021 0.001 TYR S 235 ARG 0.002 0.000 ARG R 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 133 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7947 (mtmm) cc_final: 0.7615 (ptpt) REVERT: R 101 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7187 (mtt-85) REVERT: R 106 MET cc_start: 0.8642 (tpp) cc_final: 0.8175 (mmp) REVERT: R 227 LYS cc_start: 0.7881 (ptpt) cc_final: 0.7645 (ptpp) REVERT: A 276 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: A 313 ARG cc_start: 0.5981 (OUTLIER) cc_final: 0.5387 (pmm-80) REVERT: S 43 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8790 (mmmt) REVERT: S 235 TYR cc_start: 0.7320 (OUTLIER) cc_final: 0.6893 (t80) REVERT: B 52 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8095 (mtt90) REVERT: B 195 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7481 (p0) REVERT: B 197 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6880 (mtt-85) REVERT: B 293 ASN cc_start: 0.8277 (m-40) cc_final: 0.7963 (m-40) outliers start: 44 outliers final: 23 residues processed: 158 average time/residue: 1.0964 time to fit residues: 185.9098 Evaluate side-chains 159 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 129 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 64 optimal weight: 0.0010 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 GLN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8904 Z= 0.186 Angle : 0.512 8.985 12084 Z= 0.267 Chirality : 0.041 0.170 1377 Planarity : 0.003 0.047 1524 Dihedral : 5.186 85.890 1237 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.84 % Allowed : 28.79 % Favored : 66.37 % 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: 0.52 (0.25), residues: 1115 helix: 2.17 (0.27), residues: 362 sheet: 0.23 (0.30), residues: 267 loop : -1.02 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.016 0.001 PHE A 334 TYR 0.021 0.001 TYR S 235 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 132 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7959 (mtmm) cc_final: 0.7665 (ptpt) REVERT: R 101 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7241 (mtt-85) REVERT: A 15 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.6502 (ttt-90) REVERT: A 257 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.7911 (ptmt) REVERT: A 276 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: A 313 ARG cc_start: 0.6008 (OUTLIER) cc_final: 0.5429 (pmm-80) REVERT: S 235 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.6940 (t80) REVERT: B 52 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8094 (mtt90) REVERT: B 195 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7464 (p0) REVERT: B 197 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6897 (mtt-85) REVERT: B 293 ASN cc_start: 0.8296 (m-40) cc_final: 0.7985 (m-40) outliers start: 44 outliers final: 28 residues processed: 160 average time/residue: 1.1103 time to fit residues: 190.3166 Evaluate side-chains 163 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 126 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 50.0000 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 GLN S 39 GLN S 179 GLN S 183 GLN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8904 Z= 0.375 Angle : 0.618 10.378 12084 Z= 0.320 Chirality : 0.045 0.215 1377 Planarity : 0.004 0.046 1524 Dihedral : 5.706 88.476 1237 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 5.16 % Allowed : 28.57 % Favored : 66.26 % 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: 0.34 (0.25), residues: 1115 helix: 1.96 (0.27), residues: 357 sheet: 0.15 (0.30), residues: 271 loop : -1.06 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 63 HIS 0.005 0.001 HIS A 188 PHE 0.016 0.002 PHE S 27 TYR 0.027 0.002 TYR S 235 ARG 0.005 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 132 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7954 (mtmm) cc_final: 0.7646 (ptpt) REVERT: R 101 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7232 (mtt-85) REVERT: R 112 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8510 (mt0) REVERT: A 15 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.6616 (ttt-90) REVERT: A 257 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.7915 (ptmt) REVERT: A 276 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: A 313 ARG cc_start: 0.6077 (OUTLIER) cc_final: 0.5486 (pmm-80) REVERT: S 172 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8546 (t) REVERT: S 235 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.7089 (t80) REVERT: B 52 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8122 (mtt90) REVERT: B 195 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7468 (p0) REVERT: B 197 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6934 (mtt-85) REVERT: B 260 GLU cc_start: 0.8714 (tt0) cc_final: 0.8479 (tt0) outliers start: 47 outliers final: 28 residues processed: 164 average time/residue: 1.0864 time to fit residues: 191.1574 Evaluate side-chains 166 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 127 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 64 optimal weight: 0.3980 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 GLN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8904 Z= 0.172 Angle : 0.530 11.139 12084 Z= 0.274 Chirality : 0.041 0.175 1377 Planarity : 0.004 0.108 1524 Dihedral : 5.329 85.752 1237 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.84 % Allowed : 28.68 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.25), residues: 1115 helix: 2.09 (0.28), residues: 363 sheet: 0.25 (0.31), residues: 261 loop : -1.10 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS A 322 PHE 0.016 0.001 PHE A 334 TYR 0.023 0.001 TYR S 235 ARG 0.002 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 130 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 11 LEU cc_start: 0.6502 (OUTLIER) cc_final: 0.6291 (tt) REVERT: R 28 LYS cc_start: 0.7944 (mtmm) cc_final: 0.7644 (ptpt) REVERT: R 101 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7139 (mtt-85) REVERT: R 112 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8435 (mt0) REVERT: A 15 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.6511 (ttt-90) REVERT: A 257 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.7946 (ptmt) REVERT: A 276 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7211 (mp0) REVERT: A 313 ARG cc_start: 0.5998 (OUTLIER) cc_final: 0.5347 (pmm-80) REVERT: S 235 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.6864 (t80) REVERT: B 52 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8118 (mtt90) REVERT: B 195 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7464 (p0) REVERT: B 197 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6908 (mtt-85) REVERT: B 293 ASN cc_start: 0.8335 (m-40) cc_final: 0.8007 (m-40) outliers start: 44 outliers final: 28 residues processed: 157 average time/residue: 1.1630 time to fit residues: 195.0929 Evaluate side-chains 166 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 127 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.5980 chunk 72 optimal weight: 50.0000 chunk 109 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 0.0070 chunk 69 optimal weight: 0.2980 chunk 92 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 GLN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8904 Z= 0.147 Angle : 0.523 12.090 12084 Z= 0.268 Chirality : 0.041 0.151 1377 Planarity : 0.004 0.111 1524 Dihedral : 5.060 84.331 1237 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.29 % Allowed : 29.34 % Favored : 66.37 % 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: 0.53 (0.25), residues: 1115 helix: 2.25 (0.27), residues: 363 sheet: 0.23 (0.31), residues: 263 loop : -1.07 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.000 HIS A 322 PHE 0.018 0.001 PHE A 334 TYR 0.019 0.001 TYR S 235 ARG 0.002 0.000 ARG R 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 134 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7949 (mtmm) cc_final: 0.7649 (ptpt) REVERT: R 101 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.7057 (mpt-90) REVERT: R 112 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8388 (mt0) REVERT: A 15 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.6622 (ttt-90) REVERT: A 276 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: A 313 ARG cc_start: 0.5976 (OUTLIER) cc_final: 0.5325 (pmm-80) REVERT: S 213 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7765 (p) REVERT: S 235 TYR cc_start: 0.7193 (OUTLIER) cc_final: 0.6868 (t80) REVERT: B 52 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8118 (mtt90) REVERT: B 195 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7474 (p0) REVERT: B 197 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6930 (mtt-85) REVERT: B 293 ASN cc_start: 0.8190 (m-40) cc_final: 0.7898 (m-40) outliers start: 39 outliers final: 22 residues processed: 159 average time/residue: 1.1233 time to fit residues: 191.3499 Evaluate side-chains 162 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 130 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 89 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 GLN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.166504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.126994 restraints weight = 10037.307| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.99 r_work: 0.3260 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8904 Z= 0.224 Angle : 0.559 12.179 12084 Z= 0.287 Chirality : 0.042 0.174 1377 Planarity : 0.004 0.108 1524 Dihedral : 5.254 86.389 1237 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.74 % Allowed : 30.33 % Favored : 65.93 % 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: 0.47 (0.25), residues: 1115 helix: 2.15 (0.27), residues: 363 sheet: 0.25 (0.31), residues: 261 loop : -1.09 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 322 PHE 0.020 0.001 PHE A 334 TYR 0.021 0.001 TYR S 235 ARG 0.003 0.000 ARG B 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3789.65 seconds wall clock time: 67 minutes 58.31 seconds (4078.31 seconds total)