Starting phenix.real_space_refine on Thu Jun 27 05:34:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unj_42406/06_2024/8unj_42406_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unj_42406/06_2024/8unj_42406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unj_42406/06_2024/8unj_42406.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unj_42406/06_2024/8unj_42406.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unj_42406/06_2024/8unj_42406_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unj_42406/06_2024/8unj_42406_updated.pdb" } resolution = 3.35 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= 0.041 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: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 3 5.21 5 S 75 5.16 5 C 7496 2.51 5 N 2087 2.21 5 O 2244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 214": "NH1" <-> "NH2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "D GLU 218": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 11916 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1374 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2514 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 13, 'TRANS': 305} Chain: "C" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2591 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "D" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2541 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 315} Chain: "E" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2773 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.40, per 1000 atoms: 0.62 Number of scatterers: 11916 At special positions: 0 Unit cell: (94.392, 110.952, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 75 16.00 P 11 15.00 Mg 3 11.99 O 2244 8.00 N 2087 7.00 C 7496 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.99 Conformation dependent library (CDL) restraints added in 2.3 seconds 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2852 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 7 sheets defined 54.7% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 722 through 742 Processing helix chain 'A' and resid 746 through 749 No H-bonds generated for 'chain 'A' and resid 746 through 749' Processing helix chain 'A' and resid 754 through 759 Processing helix chain 'A' and resid 763 through 768 Processing helix chain 'A' and resid 783 through 798 Processing helix chain 'A' and resid 838 through 862 Processing helix chain 'B' and resid 38 through 41 No H-bonds generated for 'chain 'B' and resid 38 through 41' Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 54 through 66 Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'B' and resid 115 through 118 No H-bonds generated for 'chain 'B' and resid 115 through 118' Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 148 through 163 removed outlier: 3.708A pdb=" N ARG B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LYS B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 195 through 209 removed outlier: 3.649A pdb=" N ARG B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 225 Processing helix chain 'B' and resid 229 through 242 Processing helix chain 'B' and resid 248 through 254 Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 275 through 287 Processing helix chain 'B' and resid 292 through 304 Processing helix chain 'B' and resid 310 through 329 Processing helix chain 'B' and resid 334 through 348 removed outlier: 3.790A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 25 No H-bonds generated for 'chain 'C' and resid 22 through 25' Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.591A pdb=" N GLU C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'C' and resid 98 through 101 No H-bonds generated for 'chain 'C' and resid 98 through 101' Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 127 through 129 No H-bonds generated for 'chain 'C' and resid 127 through 129' Processing helix chain 'C' and resid 132 through 144 removed outlier: 4.025A pdb=" N ARG C 139 " --> pdb=" O GLN C 135 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ARG C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 163 through 168 Processing helix chain 'C' and resid 183 through 193 Processing helix chain 'C' and resid 199 through 207 Processing helix chain 'C' and resid 216 through 226 Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 244 through 256 removed outlier: 3.970A pdb=" N MET C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 272 Processing helix chain 'C' and resid 277 through 290 removed outlier: 3.762A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 312 Processing helix chain 'C' and resid 318 through 339 removed outlier: 3.634A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 56 through 67 Processing helix chain 'D' and resid 84 through 96 removed outlier: 4.018A pdb=" N ILE D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 104 No H-bonds generated for 'chain 'D' and resid 101 through 104' Processing helix chain 'D' and resid 116 through 127 removed outlier: 4.208A pdb=" N VAL D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 161 Processing helix chain 'D' and resid 163 through 169 Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 204 through 217 removed outlier: 3.557A pdb=" N GLN D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG D 210 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU D 211 " --> pdb=" O GLN D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 234 Processing helix chain 'D' and resid 238 through 252 Processing helix chain 'D' and resid 259 through 265 Processing helix chain 'D' and resid 271 through 283 removed outlier: 3.544A pdb=" N GLN D 282 " --> pdb=" O PHE D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 298 Processing helix chain 'D' and resid 303 through 315 Processing helix chain 'D' and resid 321 through 340 Processing helix chain 'D' and resid 344 through 359 Processing helix chain 'E' and resid 13 through 15 No H-bonds generated for 'chain 'E' and resid 13 through 15' Processing helix chain 'E' and resid 20 through 31 Processing helix chain 'E' and resid 48 through 59 Processing helix chain 'E' and resid 97 through 109 removed outlier: 6.611A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP E 104 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG E 105 " --> pdb=" O ASN E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 116 Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 148 through 154 Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 through 170' Processing helix chain 'E' and resid 173 through 178 removed outlier: 3.886A pdb=" N ARG E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 202 Processing helix chain 'E' and resid 209 through 219 removed outlier: 3.651A pdb=" N SER E 219 " --> pdb=" O LEU E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 236 Processing helix chain 'E' and resid 250 through 264 Processing helix chain 'E' and resid 268 through 283 Processing helix chain 'E' and resid 288 through 299 Processing helix chain 'E' and resid 308 through 324 Processing helix chain 'E' and resid 329 through 348 Processing sheet with id= A, first strand: chain 'A' and resid 179 through 181 Processing sheet with id= B, first strand: chain 'A' and resid 803 through 807 Processing sheet with id= C, first strand: chain 'B' and resid 186 through 190 removed outlier: 3.512A pdb=" N ILE B 73 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY B 76 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 170 through 174 removed outlier: 4.022A pdb=" N GLY C 60 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS C 120 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N CYS C 152 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL C 122 " --> pdb=" O CYS C 152 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE C 154 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU C 124 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 195 through 199 removed outlier: 3.680A pdb=" N TYR D 77 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY D 78 " --> pdb=" O CYS D 180 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LYS D 145 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N CYS D 177 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU D 149 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 162 through 164 removed outlier: 6.693A pdb=" N LEU E 38 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU E 180 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N TYR E 41 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL E 182 " --> pdb=" O TYR E 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'E' and resid 68 through 75 removed outlier: 6.331A pdb=" N VAL E 131 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL E 95 " --> pdb=" O VAL E 131 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU E 133 " --> pdb=" O VAL E 95 " (cutoff:3.500A) 539 hydrogen bonds defined for protein. 1584 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: 3.15 Time building geometry restraints manager: 5.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 4005 1.37 - 1.51: 3171 1.51 - 1.66: 4823 1.66 - 1.80: 76 1.80 - 1.95: 34 Bond restraints: 12109 Sorted by residual: bond pdb=" C GLN D 208 " pdb=" O GLN D 208 " ideal model delta sigma weight residual 1.236 1.286 -0.050 1.15e-02 7.56e+03 1.88e+01 bond pdb=" N ILE E 329 " pdb=" CA ILE E 329 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.08e+00 bond pdb=" N GLN D 208 " pdb=" CA GLN D 208 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.40e+00 bond pdb=" N ALA D 215 " pdb=" CA ALA D 215 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 6.09e+00 bond pdb=" N LEU D 211 " pdb=" CA LEU D 211 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.28e-02 6.10e+03 6.07e+00 ... (remaining 12104 not shown) Histogram of bond angle deviations from ideal: 100.23 - 107.29: 428 107.29 - 114.35: 7202 114.35 - 121.40: 5866 121.40 - 128.46: 2837 128.46 - 135.51: 61 Bond angle restraints: 16394 Sorted by residual: angle pdb=" N ASN D 181 " pdb=" CA ASN D 181 " pdb=" C ASN D 181 " ideal model delta sigma weight residual 113.16 105.52 7.64 1.24e+00 6.50e-01 3.79e+01 angle pdb=" C GLN D 207 " pdb=" N GLN D 208 " pdb=" CA GLN D 208 " ideal model delta sigma weight residual 120.44 113.54 6.90 1.30e+00 5.92e-01 2.82e+01 angle pdb=" N GLU D 218 " pdb=" CA GLU D 218 " pdb=" C GLU D 218 " ideal model delta sigma weight residual 113.19 107.56 5.63 1.19e+00 7.06e-01 2.24e+01 angle pdb=" N ILE D 214 " pdb=" CA ILE D 214 " pdb=" C ILE D 214 " ideal model delta sigma weight residual 110.42 106.01 4.41 9.60e-01 1.09e+00 2.11e+01 angle pdb=" N LEU D 211 " pdb=" CA LEU D 211 " pdb=" C LEU D 211 " ideal model delta sigma weight residual 111.82 106.82 5.00 1.16e+00 7.43e-01 1.86e+01 ... (remaining 16389 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.71: 7045 23.71 - 47.42: 400 47.42 - 71.13: 68 71.13 - 94.84: 8 94.84 - 118.54: 3 Dihedral angle restraints: 7524 sinusoidal: 3144 harmonic: 4380 Sorted by residual: dihedral pdb=" C5' ADP E2000 " pdb=" O5' ADP E2000 " pdb=" PA ADP E2000 " pdb=" O2A ADP E2000 " ideal model delta sinusoidal sigma weight residual -60.00 -178.54 118.54 1 2.00e+01 2.50e-03 3.55e+01 dihedral pdb=" O1B ADP E2000 " pdb=" O3A ADP E2000 " pdb=" PB ADP E2000 " pdb=" PA ADP E2000 " ideal model delta sinusoidal sigma weight residual -60.00 52.99 -112.99 1 2.00e+01 2.50e-03 3.34e+01 dihedral pdb=" CA HIS C 241 " pdb=" C HIS C 241 " pdb=" N PRO C 242 " pdb=" CA PRO C 242 " ideal model delta harmonic sigma weight residual -180.00 -157.71 -22.29 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 7521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1388 0.043 - 0.086: 391 0.086 - 0.129: 112 0.129 - 0.172: 18 0.172 - 0.215: 6 Chirality restraints: 1915 Sorted by residual: chirality pdb=" CA LEU D 212 " pdb=" N LEU D 212 " pdb=" C LEU D 212 " pdb=" CB LEU D 212 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ILE D 214 " pdb=" N ILE D 214 " pdb=" C ILE D 214 " pdb=" CB ILE D 214 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA LEU E 67 " pdb=" N LEU E 67 " pdb=" C LEU E 67 " pdb=" CB LEU E 67 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 1912 not shown) Planarity restraints: 2080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 173 " 0.067 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO E 174 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO E 174 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO E 174 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 257 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO B 258 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 258 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 258 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 267 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.12e+00 pdb=" N PRO E 268 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 268 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 268 " 0.031 5.00e-02 4.00e+02 ... (remaining 2077 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 172 2.65 - 3.21: 10392 3.21 - 3.77: 19564 3.77 - 4.34: 25552 4.34 - 4.90: 41578 Nonbonded interactions: 97258 Sorted by model distance: nonbonded pdb="MG MG D 401 " pdb=" O2B AGS D 402 " model vdw 2.083 2.170 nonbonded pdb="MG MG C 401 " pdb=" O3G AGS C 402 " model vdw 2.087 2.170 nonbonded pdb="MG MG B 401 " pdb=" O2G AGS B 402 " model vdw 2.116 2.170 nonbonded pdb=" OG1 THR B 83 " pdb="MG MG B 401 " model vdw 2.119 2.170 nonbonded pdb="MG MG D 401 " pdb=" O2G AGS D 402 " model vdw 2.197 2.170 ... (remaining 97253 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: 3.150 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: 0.020 Extract box with map and model: 7.210 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.960 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5760 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12109 Z= 0.223 Angle : 0.700 10.070 16394 Z= 0.411 Chirality : 0.045 0.215 1915 Planarity : 0.007 0.101 2080 Dihedral : 14.943 118.544 4672 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.51 % Allowed : 9.39 % Favored : 87.10 % 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: -1.77 (0.19), residues: 1481 helix: -1.30 (0.15), residues: 879 sheet: -0.63 (0.41), residues: 143 loop : -0.63 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 253 HIS 0.005 0.001 HIS E 19 PHE 0.014 0.001 PHE E 339 TYR 0.020 0.001 TYR E 41 ARG 0.004 0.000 ARG C 215 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 246 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 MET cc_start: -0.2409 (ttm) cc_final: -0.3480 (ptm) REVERT: B 185 CYS cc_start: 0.2644 (m) cc_final: 0.2287 (m) REVERT: C 202 MET cc_start: 0.5514 (tmm) cc_final: 0.5016 (tmm) REVERT: C 206 VAL cc_start: 0.7070 (OUTLIER) cc_final: 0.6861 (p) REVERT: D 77 TYR cc_start: 0.3767 (p90) cc_final: 0.3194 (p90) REVERT: D 227 ILE cc_start: 0.7255 (tt) cc_final: 0.7054 (tt) REVERT: D 304 THR cc_start: 0.7812 (OUTLIER) cc_final: 0.7581 (p) outliers start: 46 outliers final: 12 residues processed: 278 average time/residue: 0.2299 time to fit residues: 91.0421 Evaluate side-chains 179 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 165 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 314 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 69 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 GLN A 820 ASN B 126 GLN B 237 GLN B 268 GLN C 32 ASN C 38 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 HIS D 73 ASN ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN E 206 ASN E 265 GLN E 269 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5875 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12109 Z= 0.164 Angle : 0.544 10.535 16394 Z= 0.270 Chirality : 0.038 0.136 1915 Planarity : 0.005 0.083 2080 Dihedral : 10.010 106.615 1722 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.82 % Allowed : 15.34 % Favored : 81.83 % 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: -0.66 (0.21), residues: 1481 helix: -0.28 (0.17), residues: 888 sheet: -0.75 (0.41), residues: 144 loop : -0.26 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 40 HIS 0.005 0.001 HIS D 311 PHE 0.014 0.001 PHE C 119 TYR 0.023 0.001 TYR B 279 ARG 0.005 0.000 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 168 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 830 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5907 (tt) REVERT: B 158 MET cc_start: -0.3570 (ttm) cc_final: -0.4488 (ptm) REVERT: B 340 LEU cc_start: 0.6264 (tt) cc_final: 0.5997 (tt) REVERT: C 202 MET cc_start: 0.5460 (tmm) cc_final: 0.5060 (tmm) REVERT: D 77 TYR cc_start: 0.3770 (p90) cc_final: 0.3296 (p90) REVERT: D 304 THR cc_start: 0.7837 (OUTLIER) cc_final: 0.7624 (p) outliers start: 37 outliers final: 19 residues processed: 197 average time/residue: 0.2197 time to fit residues: 63.7853 Evaluate side-chains 183 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 162 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 143 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 ASN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 HIS ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6018 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12109 Z= 0.225 Angle : 0.577 11.179 16394 Z= 0.285 Chirality : 0.040 0.140 1915 Planarity : 0.005 0.076 2080 Dihedral : 9.573 110.489 1706 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.36 % Allowed : 15.50 % Favored : 81.15 % 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: -0.17 (0.22), residues: 1481 helix: 0.15 (0.17), residues: 885 sheet: -0.88 (0.40), residues: 144 loop : -0.01 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 40 HIS 0.005 0.001 HIS C 241 PHE 0.015 0.002 PHE E 35 TYR 0.022 0.002 TYR B 279 ARG 0.008 0.000 ARG D 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 176 time to evaluate : 1.527 Fit side-chains revert: symmetry clash REVERT: A 727 GLN cc_start: 0.7993 (tp-100) cc_final: 0.7644 (pp30) REVERT: A 815 TYR cc_start: 0.4421 (m-80) cc_final: 0.3923 (m-80) REVERT: A 855 ARG cc_start: 0.6905 (mmm160) cc_final: 0.6624 (mmm160) REVERT: B 158 MET cc_start: -0.3443 (ttm) cc_final: -0.4428 (ptm) REVERT: B 185 CYS cc_start: 0.2574 (m) cc_final: 0.2082 (m) REVERT: B 229 MET cc_start: 0.4340 (tpp) cc_final: 0.4113 (tpp) REVERT: C 202 MET cc_start: 0.5639 (tmm) cc_final: 0.5296 (tmm) REVERT: D 77 TYR cc_start: 0.3920 (p90) cc_final: 0.3412 (p90) REVERT: D 304 THR cc_start: 0.7869 (OUTLIER) cc_final: 0.7647 (p) REVERT: E 108 ILE cc_start: 0.7562 (mm) cc_final: 0.7196 (mt) REVERT: E 262 ILE cc_start: 0.6924 (mm) cc_final: 0.6663 (mt) outliers start: 44 outliers final: 28 residues processed: 203 average time/residue: 0.2057 time to fit residues: 62.6779 Evaluate side-chains 183 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 303 CYS Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 732 GLN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 GLN B 135 HIS B 237 GLN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 GLN ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS E 206 ASN ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6086 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12109 Z= 0.252 Angle : 0.593 10.636 16394 Z= 0.294 Chirality : 0.040 0.145 1915 Planarity : 0.005 0.072 2080 Dihedral : 9.338 112.444 1701 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.97 % Allowed : 16.56 % Favored : 79.47 % 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: 0.00 (0.22), residues: 1481 helix: 0.32 (0.18), residues: 873 sheet: -1.05 (0.40), residues: 142 loop : 0.08 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 40 HIS 0.005 0.001 HIS C 241 PHE 0.015 0.002 PHE E 346 TYR 0.014 0.002 TYR E 279 ARG 0.003 0.000 ARG E 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 174 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: A 727 GLN cc_start: 0.8047 (tp-100) cc_final: 0.7674 (pp30) REVERT: A 815 TYR cc_start: 0.4516 (m-80) cc_final: 0.4136 (m-80) REVERT: A 855 ARG cc_start: 0.6948 (mmm160) cc_final: 0.6716 (mmm160) REVERT: B 146 MET cc_start: 0.1528 (ttt) cc_final: 0.0775 (mtp) REVERT: B 158 MET cc_start: -0.3448 (ttm) cc_final: -0.4328 (ptm) REVERT: B 229 MET cc_start: 0.4284 (tpp) cc_final: 0.4022 (tpp) REVERT: C 122 VAL cc_start: 0.7660 (t) cc_final: 0.7175 (m) REVERT: C 202 MET cc_start: 0.5734 (tmm) cc_final: 0.5370 (tmm) REVERT: D 77 TYR cc_start: 0.4014 (p90) cc_final: 0.3531 (p90) REVERT: D 304 THR cc_start: 0.7894 (OUTLIER) cc_final: 0.7669 (p) REVERT: E 108 ILE cc_start: 0.7693 (mm) cc_final: 0.7340 (mt) outliers start: 52 outliers final: 37 residues processed: 208 average time/residue: 0.2146 time to fit residues: 66.0445 Evaluate side-chains 194 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 156 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 303 CYS Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 732 GLN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 12109 Z= 0.337 Angle : 0.681 10.128 16394 Z= 0.335 Chirality : 0.043 0.161 1915 Planarity : 0.005 0.070 2080 Dihedral : 9.440 113.482 1701 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.66 % Allowed : 17.40 % Favored : 77.94 % 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: -0.22 (0.22), residues: 1481 helix: 0.16 (0.18), residues: 866 sheet: -1.13 (0.41), residues: 137 loop : -0.08 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 40 HIS 0.012 0.002 HIS B 135 PHE 0.018 0.002 PHE B 316 TYR 0.016 0.002 TYR D 44 ARG 0.016 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 162 time to evaluate : 1.535 Fit side-chains REVERT: A 738 GLN cc_start: 0.6122 (tp-100) cc_final: 0.5912 (tp-100) REVERT: A 815 TYR cc_start: 0.4896 (m-80) cc_final: 0.3989 (m-80) REVERT: A 855 ARG cc_start: 0.6940 (mmm160) cc_final: 0.6702 (mmm160) REVERT: B 158 MET cc_start: -0.3371 (ttm) cc_final: -0.4285 (ptm) REVERT: B 229 MET cc_start: 0.4325 (tpp) cc_final: 0.4121 (tpp) REVERT: C 122 VAL cc_start: 0.7717 (t) cc_final: 0.7363 (m) REVERT: C 202 MET cc_start: 0.5950 (tmm) cc_final: 0.5318 (tmm) REVERT: D 77 TYR cc_start: 0.4149 (p90) cc_final: 0.3669 (p90) REVERT: D 214 ILE cc_start: 0.6669 (OUTLIER) cc_final: 0.6432 (mm) REVERT: D 304 THR cc_start: 0.7928 (OUTLIER) cc_final: 0.7691 (p) REVERT: E 108 ILE cc_start: 0.7762 (mm) cc_final: 0.7496 (mt) REVERT: E 191 ASP cc_start: 0.4519 (m-30) cc_final: 0.4278 (m-30) REVERT: E 281 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7398 (tt) REVERT: E 332 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7539 (mp) outliers start: 61 outliers final: 43 residues processed: 205 average time/residue: 0.2087 time to fit residues: 64.6046 Evaluate side-chains 199 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 152 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 303 CYS Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 11 optimal weight: 0.0060 chunk 46 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 HIS B 237 GLN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12109 Z= 0.174 Angle : 0.572 10.517 16394 Z= 0.279 Chirality : 0.040 0.260 1915 Planarity : 0.004 0.069 2080 Dihedral : 9.078 109.608 1701 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.75 % Allowed : 19.77 % Favored : 77.48 % 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: 0.10 (0.22), residues: 1481 helix: 0.39 (0.18), residues: 877 sheet: -1.16 (0.41), residues: 141 loop : 0.18 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP D 40 HIS 0.009 0.001 HIS C 55 PHE 0.011 0.001 PHE D 126 TYR 0.018 0.001 TYR E 279 ARG 0.004 0.000 ARG E 224 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 170 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 727 GLN cc_start: 0.7978 (tp-100) cc_final: 0.7718 (pp30) REVERT: A 815 TYR cc_start: 0.4597 (m-80) cc_final: 0.4033 (m-80) REVERT: A 855 ARG cc_start: 0.6859 (mmm160) cc_final: 0.6602 (mmm160) REVERT: B 158 MET cc_start: -0.3395 (ttm) cc_final: -0.4272 (ptm) REVERT: B 192 LYS cc_start: 0.7641 (tptt) cc_final: 0.7366 (tptt) REVERT: C 202 MET cc_start: 0.5817 (tmm) cc_final: 0.5415 (tmm) REVERT: C 213 MET cc_start: 0.7096 (mmp) cc_final: 0.6319 (mmp) REVERT: C 292 ASP cc_start: 0.6076 (t0) cc_final: 0.5871 (t0) REVERT: D 77 TYR cc_start: 0.4076 (p90) cc_final: 0.3515 (p90) REVERT: D 304 THR cc_start: 0.7918 (OUTLIER) cc_final: 0.7710 (p) REVERT: E 108 ILE cc_start: 0.7691 (mm) cc_final: 0.7408 (mt) REVERT: E 134 LEU cc_start: 0.7101 (mt) cc_final: 0.6824 (tt) REVERT: E 191 ASP cc_start: 0.3926 (m-30) cc_final: 0.3666 (m-30) REVERT: E 278 LEU cc_start: 0.7684 (mt) cc_final: 0.7479 (mt) REVERT: E 281 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7342 (tt) outliers start: 36 outliers final: 29 residues processed: 200 average time/residue: 0.1939 time to fit residues: 58.6053 Evaluate side-chains 186 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 155 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 118 optimal weight: 0.0030 chunk 78 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6043 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12109 Z= 0.166 Angle : 0.578 10.507 16394 Z= 0.281 Chirality : 0.040 0.187 1915 Planarity : 0.004 0.068 2080 Dihedral : 8.927 111.189 1701 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.89 % Allowed : 19.54 % Favored : 76.56 % 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: 0.31 (0.22), residues: 1481 helix: 0.56 (0.18), residues: 876 sheet: -1.10 (0.41), residues: 141 loop : 0.29 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP D 40 HIS 0.004 0.001 HIS E 37 PHE 0.011 0.001 PHE E 35 TYR 0.013 0.001 TYR B 279 ARG 0.005 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 167 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 727 GLN cc_start: 0.7910 (tp-100) cc_final: 0.7680 (pp30) REVERT: A 815 TYR cc_start: 0.4567 (m-80) cc_final: 0.4175 (m-80) REVERT: A 855 ARG cc_start: 0.6873 (mmm160) cc_final: 0.6628 (mmm160) REVERT: B 158 MET cc_start: -0.3341 (ttm) cc_final: -0.4229 (ptm) REVERT: B 192 LYS cc_start: 0.7625 (tptt) cc_final: 0.7344 (tptt) REVERT: B 229 MET cc_start: 0.4143 (tpp) cc_final: 0.3559 (tpp) REVERT: B 308 MET cc_start: 0.6988 (mmm) cc_final: 0.6420 (mmt) REVERT: B 341 LEU cc_start: 0.7960 (mp) cc_final: 0.7524 (mt) REVERT: C 202 MET cc_start: 0.5734 (tmm) cc_final: 0.5120 (tmm) REVERT: C 212 ASP cc_start: 0.7014 (p0) cc_final: 0.6684 (p0) REVERT: C 292 ASP cc_start: 0.6041 (t0) cc_final: 0.5818 (t0) REVERT: D 77 TYR cc_start: 0.3970 (p90) cc_final: 0.3440 (p90) REVERT: D 304 THR cc_start: 0.7934 (OUTLIER) cc_final: 0.7731 (p) REVERT: E 108 ILE cc_start: 0.7586 (mm) cc_final: 0.7354 (mt) REVERT: E 281 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7211 (tt) outliers start: 51 outliers final: 36 residues processed: 207 average time/residue: 0.2083 time to fit residues: 64.2453 Evaluate side-chains 195 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 157 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 89 optimal weight: 0.0980 chunk 95 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 128 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 GLN E 206 ASN ** E 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12109 Z= 0.159 Angle : 0.583 10.606 16394 Z= 0.285 Chirality : 0.040 0.177 1915 Planarity : 0.004 0.068 2080 Dihedral : 8.809 113.159 1701 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.36 % Allowed : 20.00 % Favored : 76.64 % 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 (0.22), residues: 1481 helix: 0.59 (0.18), residues: 895 sheet: -1.09 (0.44), residues: 125 loop : 0.20 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP D 40 HIS 0.004 0.001 HIS E 37 PHE 0.013 0.001 PHE E 35 TYR 0.010 0.001 TYR E 155 ARG 0.009 0.000 ARG E 234 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 161 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 727 GLN cc_start: 0.7902 (tp-100) cc_final: 0.7649 (pp30) REVERT: A 815 TYR cc_start: 0.4786 (m-80) cc_final: 0.4037 (m-80) REVERT: A 855 ARG cc_start: 0.6902 (mmm160) cc_final: 0.6673 (mmm160) REVERT: B 158 MET cc_start: -0.3346 (ttm) cc_final: -0.4236 (ptm) REVERT: B 192 LYS cc_start: 0.7593 (tptt) cc_final: 0.7307 (tptt) REVERT: B 229 MET cc_start: 0.4164 (tpp) cc_final: 0.3856 (tpp) REVERT: B 341 LEU cc_start: 0.7931 (mp) cc_final: 0.7431 (mt) REVERT: C 202 MET cc_start: 0.5745 (tmm) cc_final: 0.5160 (tmm) REVERT: C 212 ASP cc_start: 0.7001 (p0) cc_final: 0.6674 (p0) REVERT: C 292 ASP cc_start: 0.5992 (t0) cc_final: 0.5788 (t0) REVERT: D 77 TYR cc_start: 0.3939 (p90) cc_final: 0.3411 (p90) REVERT: D 356 MET cc_start: 0.6962 (OUTLIER) cc_final: 0.6672 (mtp) REVERT: E 108 ILE cc_start: 0.7587 (mm) cc_final: 0.7355 (mt) REVERT: E 281 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7215 (tt) outliers start: 44 outliers final: 37 residues processed: 197 average time/residue: 0.1953 time to fit residues: 58.5525 Evaluate side-chains 195 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 156 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 302 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 118 optimal weight: 0.0170 chunk 124 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 GLN E 206 ASN ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12109 Z= 0.165 Angle : 0.612 14.681 16394 Z= 0.292 Chirality : 0.040 0.212 1915 Planarity : 0.004 0.068 2080 Dihedral : 8.650 115.072 1700 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.13 % Allowed : 20.69 % Favored : 76.18 % 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: 0.37 (0.22), residues: 1481 helix: 0.65 (0.18), residues: 892 sheet: -1.09 (0.44), residues: 125 loop : 0.13 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP D 40 HIS 0.006 0.001 HIS D 311 PHE 0.013 0.001 PHE E 35 TYR 0.010 0.001 TYR E 155 ARG 0.009 0.000 ARG E 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 163 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 727 GLN cc_start: 0.7889 (tp-100) cc_final: 0.7641 (pp30) REVERT: A 815 TYR cc_start: 0.4630 (m-80) cc_final: 0.4174 (m-80) REVERT: A 855 ARG cc_start: 0.6936 (mmm160) cc_final: 0.6734 (mmm160) REVERT: B 158 MET cc_start: -0.3342 (ttm) cc_final: -0.4237 (ptm) REVERT: B 192 LYS cc_start: 0.7605 (tptt) cc_final: 0.7316 (tptt) REVERT: B 229 MET cc_start: 0.4135 (tpp) cc_final: 0.3916 (tpp) REVERT: B 308 MET cc_start: 0.6874 (mmm) cc_final: 0.5066 (ptt) REVERT: B 341 LEU cc_start: 0.7885 (mp) cc_final: 0.7402 (mt) REVERT: C 202 MET cc_start: 0.5728 (tmm) cc_final: 0.5157 (tmm) REVERT: C 212 ASP cc_start: 0.6954 (p0) cc_final: 0.6659 (p0) REVERT: D 77 TYR cc_start: 0.3891 (p90) cc_final: 0.3399 (p90) REVERT: D 356 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.6652 (mtp) REVERT: E 108 ILE cc_start: 0.7631 (mm) cc_final: 0.7376 (mt) REVERT: E 134 LEU cc_start: 0.7107 (mt) cc_final: 0.6821 (tt) REVERT: E 278 LEU cc_start: 0.7763 (mt) cc_final: 0.7512 (mt) REVERT: E 281 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7217 (tt) outliers start: 41 outliers final: 35 residues processed: 196 average time/residue: 0.2081 time to fit residues: 61.9476 Evaluate side-chains 195 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 158 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 302 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12109 Z= 0.182 Angle : 0.624 13.038 16394 Z= 0.300 Chirality : 0.040 0.243 1915 Planarity : 0.004 0.068 2080 Dihedral : 8.540 118.294 1700 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.90 % Allowed : 20.92 % Favored : 76.18 % 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 (0.22), residues: 1481 helix: 0.65 (0.18), residues: 890 sheet: -1.09 (0.44), residues: 125 loop : 0.10 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP D 40 HIS 0.006 0.001 HIS D 311 PHE 0.014 0.001 PHE E 35 TYR 0.010 0.001 TYR E 155 ARG 0.008 0.000 ARG E 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 164 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 727 GLN cc_start: 0.7891 (tp-100) cc_final: 0.7644 (pp30) REVERT: A 815 TYR cc_start: 0.4806 (m-80) cc_final: 0.3985 (m-80) REVERT: A 855 ARG cc_start: 0.6966 (mmm160) cc_final: 0.6755 (mmm160) REVERT: B 158 MET cc_start: -0.3382 (ttm) cc_final: -0.4275 (ptm) REVERT: B 192 LYS cc_start: 0.7615 (tptt) cc_final: 0.7327 (tptt) REVERT: B 229 MET cc_start: 0.4164 (tpp) cc_final: 0.3931 (tpp) REVERT: B 308 MET cc_start: 0.6696 (mmm) cc_final: 0.5055 (ptt) REVERT: B 341 LEU cc_start: 0.7921 (mp) cc_final: 0.7400 (mt) REVERT: C 202 MET cc_start: 0.5835 (tmm) cc_final: 0.5261 (tmm) REVERT: C 212 ASP cc_start: 0.6994 (p0) cc_final: 0.6705 (p0) REVERT: D 77 TYR cc_start: 0.3960 (p90) cc_final: 0.3440 (p90) REVERT: D 356 MET cc_start: 0.6928 (OUTLIER) cc_final: 0.6675 (mtp) REVERT: E 108 ILE cc_start: 0.7657 (mm) cc_final: 0.7437 (mt) REVERT: E 278 LEU cc_start: 0.7797 (mt) cc_final: 0.7551 (mt) REVERT: E 281 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7285 (tt) outliers start: 38 outliers final: 33 residues processed: 194 average time/residue: 0.2118 time to fit residues: 61.1944 Evaluate side-chains 196 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 161 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 302 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 30.0000 chunk 116 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 0.2980 chunk 101 optimal weight: 0.8980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.215748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.178929 restraints weight = 20162.085| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 3.17 r_work: 0.4086 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12109 Z= 0.263 Angle : 0.684 10.908 16394 Z= 0.332 Chirality : 0.042 0.207 1915 Planarity : 0.005 0.068 2080 Dihedral : 8.696 124.916 1700 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.82 % Allowed : 21.37 % Favored : 75.80 % 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: 0.07 (0.22), residues: 1481 helix: 0.44 (0.17), residues: 887 sheet: -1.33 (0.43), residues: 125 loop : -0.01 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP D 40 HIS 0.006 0.001 HIS C 285 PHE 0.019 0.002 PHE E 346 TYR 0.013 0.002 TYR C 310 ARG 0.009 0.001 ARG E 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2585.69 seconds wall clock time: 46 minutes 54.12 seconds (2814.12 seconds total)