Starting phenix.real_space_refine on Sat Apr 6 02:18:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unx_42420/04_2024/8unx_42420_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unx_42420/04_2024/8unx_42420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unx_42420/04_2024/8unx_42420.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unx_42420/04_2024/8unx_42420.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unx_42420/04_2024/8unx_42420_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unx_42420/04_2024/8unx_42420_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 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 P 3 5.49 5 S 43 5.16 5 C 4297 2.51 5 N 1155 2.21 5 O 1190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 309": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "R GLU 107": "OE1" <-> "OE2" Residue "R TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 175": "NH1" <-> "NH2" Residue "R GLU 237": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6688 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1783 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 244, 1771 Classifications: {'peptide': 244} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 6, 'TRANS': 237} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 1, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 179 Conformer: "B" Number of residues, atoms: 244, 1771 Classifications: {'peptide': 244} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 6, 'TRANS': 237} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 1, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 179 bond proxies already assigned to first conformer: 1792 Chain: "B" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2400 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 3, 'ASP:plan': 15, 'ASN%COO:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 142 Chain: "G" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 339 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "R" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2119 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 123 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 360 " occ=0.51 ... (22 atoms not shown) pdb=" OH BTYR A 360 " occ=0.49 Time building chain proxies: 5.02, per 1000 atoms: 0.75 Number of scatterers: 6688 At special positions: 0 Unit cell: (85.0346, 134.493, 98.9178, 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) S 43 16.00 P 3 15.00 O 1190 8.00 N 1155 7.00 C 4297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.04 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.04 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: 2.70 Conformation dependent library (CDL) restraints added in 1.6 seconds 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1750 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 8 sheets defined 42.6% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 10 through 39 removed outlier: 3.506A pdb=" N ASN A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 60 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.609A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 349 removed outlier: 3.642A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 5 through 24 removed outlier: 3.792A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'R' and resid 29 through 60 removed outlier: 3.518A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU R 42 " --> pdb=" O ILE R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 96 removed outlier: 4.524A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 103 through 136 removed outlier: 3.660A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 170 removed outlier: 3.723A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 179 through 186 removed outlier: 3.768A pdb=" N CYS R 184 " --> pdb=" O GLU R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 207 Processing helix chain 'R' and resid 209 through 237 Processing helix chain 'R' and resid 269 through 298 removed outlier: 3.879A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.031A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 326 removed outlier: 4.187A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 338 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.311A pdb=" N VAL A 287 " --> pdb=" O ATYR A 360 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.711A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 71 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.945A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.959A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.805A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.797A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.733A pdb=" N THR B 274 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.902A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 966 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: 1.69 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2153 1.34 - 1.46: 1611 1.46 - 1.59: 3005 1.59 - 1.71: 5 1.71 - 1.84: 60 Bond restraints: 6834 Sorted by residual: bond pdb=" CA SER A 51 " pdb=" CB SER A 51 " ideal model delta sigma weight residual 1.526 1.482 0.044 1.36e-02 5.41e+03 1.04e+01 bond pdb=" N LYS B 127 " pdb=" CA LYS B 127 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.23e-02 6.61e+03 1.02e+01 bond pdb=" N ILE A 257 " pdb=" CA ILE A 257 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.19e-02 7.06e+03 8.58e+00 bond pdb=" N VAL A 256 " pdb=" CA VAL A 256 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.17e-02 7.31e+03 8.22e+00 bond pdb=" N GLU A 259 " pdb=" CA GLU A 259 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.23e-02 6.61e+03 8.00e+00 ... (remaining 6829 not shown) Histogram of bond angle deviations from ideal: 99.96 - 106.84: 165 106.84 - 113.72: 3860 113.72 - 120.59: 2968 120.59 - 127.47: 2289 127.47 - 134.35: 77 Bond angle restraints: 9359 Sorted by residual: angle pdb=" C ASN B 132 " pdb=" CA ASN B 132 " pdb=" CB ASN B 132 " ideal model delta sigma weight residual 116.63 104.25 12.38 1.16e+00 7.43e-01 1.14e+02 angle pdb=" N ARG A 13 " pdb=" CA ARG A 13 " pdb=" C ARG A 13 " ideal model delta sigma weight residual 111.28 104.48 6.80 1.09e+00 8.42e-01 3.89e+01 angle pdb=" N ASN A 23 " pdb=" CA ASN A 23 " pdb=" C ASN A 23 " ideal model delta sigma weight residual 111.28 104.91 6.37 1.09e+00 8.42e-01 3.42e+01 angle pdb=" N ARG G 13 " pdb=" CA ARG G 13 " pdb=" C ARG G 13 " ideal model delta sigma weight residual 111.28 104.97 6.31 1.09e+00 8.42e-01 3.35e+01 angle pdb=" CA ASN B 132 " pdb=" C ASN B 132 " pdb=" N VAL B 133 " ideal model delta sigma weight residual 119.63 115.23 4.40 8.10e-01 1.52e+00 2.95e+01 ... (remaining 9354 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.82: 3881 31.82 - 63.64: 61 63.64 - 95.46: 3 95.46 - 127.28: 0 127.28 - 159.10: 4 Dihedral angle restraints: 3949 sinusoidal: 1251 harmonic: 2698 Sorted by residual: dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -131.63 -159.10 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" O3B GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PB GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual -68.92 83.92 -152.84 1 2.00e+01 2.50e-03 4.54e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -43.86 148.46 1 2.00e+01 2.50e-03 4.45e+01 ... (remaining 3946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 796 0.047 - 0.094: 206 0.094 - 0.141: 78 0.141 - 0.188: 29 0.188 - 0.235: 13 Chirality restraints: 1122 Sorted by residual: chirality pdb=" CA GLU A 15 " pdb=" N GLU A 15 " pdb=" C GLU A 15 " pdb=" CB GLU A 15 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ILE G 9 " pdb=" N ILE G 9 " pdb=" C ILE G 9 " pdb=" CB ILE G 9 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ILE R 334 " pdb=" N ILE R 334 " pdb=" C ILE R 334 " pdb=" CB ILE R 334 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1119 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 125 " 0.017 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ASN B 125 " -0.061 2.00e-02 2.50e+03 pdb=" O ASN B 125 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU B 126 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 47 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.79e+00 pdb=" C GLY A 47 " 0.045 2.00e-02 2.50e+03 pdb=" O GLY A 47 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 48 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 175 " 0.012 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C ARG R 175 " -0.045 2.00e-02 2.50e+03 pdb=" O ARG R 175 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA R 176 " 0.015 2.00e-02 2.50e+03 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 325 2.72 - 3.27: 6756 3.27 - 3.81: 10425 3.81 - 4.36: 11831 4.36 - 4.90: 21028 Nonbonded interactions: 50365 Sorted by model distance: nonbonded pdb=" O LEU R 339 " pdb=" CD1 LEU R 339 " model vdw 2.177 3.460 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.250 2.440 nonbonded pdb=" OH TYR R 185 " pdb=" O PHE R 194 " model vdw 2.262 2.440 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.284 2.440 nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.296 2.440 ... (remaining 50360 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.690 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 23.290 Find NCS groups from input model: 0.200 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 : 0.006 0.053 6834 Z= 0.404 Angle : 0.964 12.378 9359 Z= 0.666 Chirality : 0.057 0.235 1122 Planarity : 0.006 0.098 1176 Dihedral : 13.805 159.097 2193 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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: 1.34 (0.27), residues: 914 helix: 2.15 (0.26), residues: 392 sheet: 1.12 (0.42), residues: 169 loop : -0.69 (0.29), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.002 PHE A 222 TYR 0.020 0.001 TYR R 185 ARG 0.012 0.001 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.888 Fit side-chains REVERT: A 253 TYR cc_start: 0.8595 (p90) cc_final: 0.8341 (p90) REVERT: A 255 MET cc_start: 0.7332 (tpp) cc_final: 0.7016 (mmm) REVERT: A 308 ILE cc_start: 0.7204 (mm) cc_final: 0.6876 (mm) REVERT: B 125 ASN cc_start: 0.9072 (t0) cc_final: 0.8832 (t0) REVERT: R 191 CYS cc_start: 0.6374 (t) cc_final: 0.6135 (t) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1824 time to fit residues: 26.8381 Evaluate side-chains 86 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 70 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6834 Z= 0.162 Angle : 0.504 8.865 9359 Z= 0.270 Chirality : 0.040 0.137 1122 Planarity : 0.003 0.038 1176 Dihedral : 10.319 146.995 1014 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.84 % Allowed : 8.40 % Favored : 90.76 % 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: 1.55 (0.27), residues: 914 helix: 2.34 (0.26), residues: 406 sheet: 0.99 (0.40), residues: 176 loop : -0.62 (0.29), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE A 222 TYR 0.008 0.001 TYR R 308 ARG 0.008 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 253 TYR cc_start: 0.8495 (p90) cc_final: 0.8182 (p90) REVERT: A 255 MET cc_start: 0.7131 (tpp) cc_final: 0.6882 (mmm) REVERT: A 308 ILE cc_start: 0.7247 (mm) cc_final: 0.6864 (mm) REVERT: B 325 MET cc_start: 0.8342 (mmt) cc_final: 0.8137 (mmt) outliers start: 5 outliers final: 5 residues processed: 101 average time/residue: 0.1708 time to fit residues: 23.6199 Evaluate side-chains 94 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6834 Z= 0.172 Angle : 0.478 6.285 9359 Z= 0.256 Chirality : 0.040 0.137 1122 Planarity : 0.003 0.036 1176 Dihedral : 9.340 145.198 1014 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.34 % Allowed : 10.59 % Favored : 88.07 % 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: 1.57 (0.28), residues: 914 helix: 2.45 (0.26), residues: 407 sheet: 0.75 (0.40), residues: 184 loop : -0.64 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.010 0.001 HIS R 93 PHE 0.016 0.001 PHE A 222 TYR 0.007 0.001 TYR R 308 ARG 0.007 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: A 253 TYR cc_start: 0.8593 (p90) cc_final: 0.8268 (p90) REVERT: A 255 MET cc_start: 0.7119 (tpp) cc_final: 0.6529 (mmm) REVERT: A 308 ILE cc_start: 0.7244 (mm) cc_final: 0.6838 (mm) REVERT: B 325 MET cc_start: 0.8342 (mmt) cc_final: 0.8131 (mmt) outliers start: 8 outliers final: 7 residues processed: 98 average time/residue: 0.1701 time to fit residues: 23.1801 Evaluate side-chains 96 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 153 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 9 optimal weight: 0.0470 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6834 Z= 0.227 Angle : 0.501 5.867 9359 Z= 0.271 Chirality : 0.041 0.144 1122 Planarity : 0.003 0.035 1176 Dihedral : 8.805 145.464 1014 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.85 % Allowed : 11.76 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.27), residues: 914 helix: 2.54 (0.26), residues: 399 sheet: 0.60 (0.39), residues: 176 loop : -0.87 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.010 0.001 HIS R 93 PHE 0.016 0.002 PHE A 222 TYR 0.009 0.001 TYR B 111 ARG 0.008 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 253 TYR cc_start: 0.8673 (p90) cc_final: 0.8389 (p90) REVERT: A 255 MET cc_start: 0.7156 (tpp) cc_final: 0.6653 (mmm) REVERT: A 308 ILE cc_start: 0.7289 (mm) cc_final: 0.6875 (mm) REVERT: A 344 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8129 (tp30) REVERT: B 325 MET cc_start: 0.8389 (mmt) cc_final: 0.8174 (mmt) outliers start: 11 outliers final: 7 residues processed: 101 average time/residue: 0.1683 time to fit residues: 23.7429 Evaluate side-chains 98 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 60 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 0.0770 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6834 Z= 0.136 Angle : 0.440 5.919 9359 Z= 0.237 Chirality : 0.039 0.143 1122 Planarity : 0.003 0.042 1176 Dihedral : 8.299 142.595 1014 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.18 % Allowed : 13.45 % Favored : 84.37 % 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: 1.56 (0.28), residues: 914 helix: 2.63 (0.26), residues: 400 sheet: 0.53 (0.38), residues: 180 loop : -0.68 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.010 0.001 HIS R 93 PHE 0.014 0.001 PHE A 222 TYR 0.007 0.001 TYR B 111 ARG 0.008 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 253 TYR cc_start: 0.8617 (p90) cc_final: 0.8318 (p90) REVERT: A 255 MET cc_start: 0.7070 (tpp) cc_final: 0.6602 (mmm) REVERT: A 308 ILE cc_start: 0.7183 (mm) cc_final: 0.6733 (mm) REVERT: A 344 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8251 (tp30) REVERT: R 142 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7533 (mm-40) outliers start: 13 outliers final: 11 residues processed: 108 average time/residue: 0.1537 time to fit residues: 23.3159 Evaluate side-chains 101 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 87 optimal weight: 0.2980 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 0.0870 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 83 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6834 Z= 0.134 Angle : 0.437 5.793 9359 Z= 0.236 Chirality : 0.039 0.143 1122 Planarity : 0.003 0.046 1176 Dihedral : 8.245 141.753 1014 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.52 % Allowed : 14.12 % Favored : 83.36 % 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: 1.52 (0.27), residues: 914 helix: 2.62 (0.26), residues: 400 sheet: 0.39 (0.38), residues: 175 loop : -0.63 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.012 0.001 HIS R 93 PHE 0.021 0.001 PHE R 289 TYR 0.006 0.001 TYR A 339 ARG 0.011 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 253 TYR cc_start: 0.8611 (p90) cc_final: 0.8339 (p90) REVERT: A 255 MET cc_start: 0.6923 (tpp) cc_final: 0.6494 (mmm) REVERT: A 308 ILE cc_start: 0.7187 (mm) cc_final: 0.6719 (mm) REVERT: A 344 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8256 (tp30) outliers start: 15 outliers final: 13 residues processed: 108 average time/residue: 0.1735 time to fit residues: 25.6210 Evaluate side-chains 108 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 93 HIS Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 0.1980 chunk 73 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6834 Z= 0.149 Angle : 0.439 5.835 9359 Z= 0.237 Chirality : 0.039 0.147 1122 Planarity : 0.003 0.051 1176 Dihedral : 8.165 145.670 1014 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.35 % Allowed : 15.13 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.28), residues: 914 helix: 2.61 (0.26), residues: 401 sheet: 0.45 (0.38), residues: 176 loop : -0.63 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.012 0.001 HIS R 93 PHE 0.013 0.001 PHE A 222 TYR 0.008 0.001 TYR B 111 ARG 0.012 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 253 TYR cc_start: 0.8618 (p90) cc_final: 0.8359 (p90) REVERT: A 255 MET cc_start: 0.6934 (tpp) cc_final: 0.6520 (mmm) REVERT: A 308 ILE cc_start: 0.7179 (mm) cc_final: 0.6722 (mm) REVERT: A 344 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8255 (tp30) REVERT: R 142 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7594 (mm-40) outliers start: 14 outliers final: 12 residues processed: 107 average time/residue: 0.1583 time to fit residues: 23.7190 Evaluate side-chains 106 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 9.9990 chunk 17 optimal weight: 0.0040 chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 0.0980 chunk 68 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6834 Z= 0.143 Angle : 0.437 6.045 9359 Z= 0.236 Chirality : 0.039 0.148 1122 Planarity : 0.003 0.050 1176 Dihedral : 8.066 155.856 1014 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.35 % Allowed : 15.29 % Favored : 82.35 % 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: 1.55 (0.27), residues: 914 helix: 2.64 (0.26), residues: 401 sheet: 0.42 (0.38), residues: 174 loop : -0.64 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.013 0.001 HIS R 93 PHE 0.012 0.001 PHE R 289 TYR 0.006 0.001 TYR B 59 ARG 0.012 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 253 TYR cc_start: 0.8632 (p90) cc_final: 0.8337 (p90) REVERT: A 255 MET cc_start: 0.6448 (tpp) cc_final: 0.6091 (mmm) REVERT: A 308 ILE cc_start: 0.7080 (mm) cc_final: 0.6579 (mm) REVERT: A 309 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6870 (mm-30) REVERT: A 344 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8263 (tp30) REVERT: R 142 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7693 (mm-40) outliers start: 14 outliers final: 11 residues processed: 107 average time/residue: 0.1572 time to fit residues: 23.6519 Evaluate side-chains 105 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 93 HIS Chi-restraints excluded: chain R residue 115 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 48 optimal weight: 0.0470 chunk 35 optimal weight: 0.0980 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 73 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 52 optimal weight: 0.3980 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 6834 Z= 0.135 Angle : 0.455 11.125 9359 Z= 0.246 Chirality : 0.039 0.150 1122 Planarity : 0.003 0.055 1176 Dihedral : 8.001 158.637 1014 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.68 % Allowed : 16.47 % Favored : 81.85 % 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: 1.58 (0.28), residues: 914 helix: 2.66 (0.26), residues: 400 sheet: 0.41 (0.39), residues: 168 loop : -0.58 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.020 0.002 HIS R 93 PHE 0.022 0.001 PHE A 222 TYR 0.008 0.001 TYR B 111 ARG 0.013 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 253 TYR cc_start: 0.8622 (p90) cc_final: 0.8328 (p90) REVERT: A 255 MET cc_start: 0.6410 (tpp) cc_final: 0.6063 (mmm) REVERT: A 308 ILE cc_start: 0.7028 (mm) cc_final: 0.6515 (mm) REVERT: A 309 GLU cc_start: 0.7476 (mm-30) cc_final: 0.6867 (mm-30) REVERT: A 344 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8289 (tp30) REVERT: R 142 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7679 (mm-40) outliers start: 10 outliers final: 8 residues processed: 107 average time/residue: 0.1584 time to fit residues: 23.6366 Evaluate side-chains 103 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.0370 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN R 93 HIS R 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6834 Z= 0.151 Angle : 0.455 9.725 9359 Z= 0.246 Chirality : 0.039 0.130 1122 Planarity : 0.003 0.052 1176 Dihedral : 7.926 163.624 1014 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.68 % Allowed : 16.30 % Favored : 82.02 % 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: 1.67 (0.28), residues: 914 helix: 2.89 (0.26), residues: 392 sheet: 0.39 (0.39), residues: 168 loop : -0.61 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.015 0.001 HIS R 93 PHE 0.015 0.001 PHE R 49 TYR 0.007 0.001 TYR B 59 ARG 0.013 0.000 ARG R 228 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.8620 (p90) cc_final: 0.8341 (p90) REVERT: A 255 MET cc_start: 0.6425 (tpp) cc_final: 0.6109 (mmm) REVERT: A 308 ILE cc_start: 0.7093 (mm) cc_final: 0.6599 (mm) REVERT: A 309 GLU cc_start: 0.7479 (mm-30) cc_final: 0.6867 (mm-30) REVERT: A 344 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8276 (tp30) REVERT: R 142 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7683 (mm-40) REVERT: R 272 LEU cc_start: 0.8063 (tp) cc_final: 0.7798 (tt) outliers start: 10 outliers final: 9 residues processed: 105 average time/residue: 0.1631 time to fit residues: 23.9775 Evaluate side-chains 101 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 93 HIS Chi-restraints excluded: chain R residue 115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.0020 chunk 10 optimal weight: 0.0040 chunk 19 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 0.0770 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.125903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.098872 restraints weight = 36323.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.102923 restraints weight = 14221.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106025 restraints weight = 7122.804| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 6834 Z= 0.137 Angle : 0.456 10.025 9359 Z= 0.246 Chirality : 0.039 0.158 1122 Planarity : 0.003 0.056 1176 Dihedral : 7.875 165.700 1014 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.34 % Allowed : 17.31 % Favored : 81.34 % 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: 1.67 (0.27), residues: 914 helix: 2.86 (0.26), residues: 392 sheet: 0.43 (0.39), residues: 168 loop : -0.59 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.014 0.001 HIS R 93 PHE 0.015 0.001 PHE R 49 TYR 0.008 0.001 TYR B 111 ARG 0.013 0.000 ARG R 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1685.93 seconds wall clock time: 31 minutes 30.27 seconds (1890.27 seconds total)