Starting phenix.real_space_refine on Sat Apr 6 02:19:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unq_42413/04_2024/8unq_42413_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unq_42413/04_2024/8unq_42413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unq_42413/04_2024/8unq_42413.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unq_42413/04_2024/8unq_42413.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unq_42413/04_2024/8unq_42413_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unq_42413/04_2024/8unq_42413_updated.pdb" } resolution = 3.3 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= 0.025 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 40 5.16 5 C 4289 2.51 5 N 1161 2.21 5 O 1194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 265": "NH1" <-> "NH2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 260": "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: 6687 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1770 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 239, 1758 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 162 Conformer: "B" Number of residues, atoms: 239, 1758 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 162 bond proxies already assigned to first conformer: 1778 Chain: "B" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2412 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 120 Chain: "G" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 343 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "R" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2114 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 122 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 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: 4.93, per 1000 atoms: 0.74 Number of scatterers: 6687 At special positions: 0 Unit cell: (85.9023, 135.361, 98.0501, 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 40 16.00 P 3 15.00 O 1194 8.00 N 1161 7.00 C 4289 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=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.5 seconds 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1738 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 8 sheets defined 43.9% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 11 through 39 removed outlier: 3.565A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 removed outlier: 3.517A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.541A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (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 317 removed outlier: 3.542A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 317' Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.568A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.518A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.507A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'R' and resid 30 through 60 removed outlier: 3.525A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 96 removed outlier: 4.266A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.560A 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: 4.114A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (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 164 removed outlier: 3.891A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 170 No H-bonds generated for 'chain 'R' and resid 167 through 170' Processing helix chain 'R' and resid 172 through 174 No H-bonds generated for 'chain 'R' and resid 172 through 174' Processing helix chain 'R' and resid 179 through 186 Processing helix chain 'R' and resid 197 through 207 removed outlier: 3.771A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 237 removed outlier: 4.115A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 298 removed outlier: 3.747A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.541A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 326 removed outlier: 3.596A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.690A 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: 7.573A pdb=" N VAL A 287 " --> pdb=" O ATYR A 360 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.751A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.193A 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: 6.935A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.750A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.882A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 262 through 264 removed outlier: 3.824A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 306 through 309 removed outlier: 3.905A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.751A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) 335 hydrogen bonds defined for protein. 978 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: 1.97 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1418 1.33 - 1.45: 1637 1.45 - 1.58: 3717 1.58 - 1.70: 5 1.70 - 1.82: 54 Bond restraints: 6831 Sorted by residual: bond pdb=" CA SER A 51 " pdb=" CB SER A 51 " ideal model delta sigma weight residual 1.528 1.473 0.055 1.59e-02 3.96e+03 1.20e+01 bond pdb=" N GLU A 50 " pdb=" CA GLU A 50 " ideal model delta sigma weight residual 1.459 1.500 -0.042 1.32e-02 5.74e+03 9.94e+00 bond pdb=" CA ALA R 271 " pdb=" CB ALA R 271 " ideal model delta sigma weight residual 1.529 1.483 0.046 1.55e-02 4.16e+03 8.65e+00 bond pdb=" N LYS A 58 " pdb=" CA LYS A 58 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.17e-02 7.31e+03 8.53e+00 bond pdb=" CA SER A 54 " pdb=" CB SER A 54 " ideal model delta sigma weight residual 1.528 1.485 0.044 1.56e-02 4.11e+03 7.88e+00 ... (remaining 6826 not shown) Histogram of bond angle deviations from ideal: 100.13 - 106.92: 154 106.92 - 113.71: 3837 113.71 - 120.50: 2637 120.50 - 127.29: 2645 127.29 - 134.08: 75 Bond angle restraints: 9348 Sorted by residual: angle pdb=" N ALA G 12 " pdb=" CA ALA G 12 " pdb=" C ALA G 12 " ideal model delta sigma weight residual 111.28 104.30 6.98 1.09e+00 8.42e-01 4.10e+01 angle pdb=" N LEU G 19 " pdb=" CA LEU G 19 " pdb=" C LEU G 19 " ideal model delta sigma weight residual 111.28 105.10 6.18 1.09e+00 8.42e-01 3.22e+01 angle pdb=" N ILE G 9 " pdb=" CA ILE G 9 " pdb=" C ILE G 9 " ideal model delta sigma weight residual 110.62 105.19 5.43 1.02e+00 9.61e-01 2.84e+01 angle pdb=" N LEU B 7 " pdb=" CA LEU B 7 " pdb=" C LEU B 7 " ideal model delta sigma weight residual 111.28 106.36 4.92 1.09e+00 8.42e-01 2.04e+01 angle pdb=" N LEU B 4 " pdb=" CA LEU B 4 " pdb=" C LEU B 4 " ideal model delta sigma weight residual 111.28 106.37 4.91 1.09e+00 8.42e-01 2.03e+01 ... (remaining 9343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.64: 3857 31.64 - 63.29: 90 63.29 - 94.93: 3 94.93 - 126.57: 1 126.57 - 158.21: 1 Dihedral angle restraints: 3952 sinusoidal: 1276 harmonic: 2676 Sorted by residual: dihedral pdb=" CB CYS R 184 " pdb=" SG CYS R 184 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual 93.00 154.11 -61.11 1 1.00e+01 1.00e-02 4.96e+01 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 -132.52 -158.21 1 2.00e+01 2.50e-03 4.63e+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 -5.32 109.91 1 2.00e+01 2.50e-03 3.22e+01 ... (remaining 3949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 810 0.044 - 0.089: 212 0.089 - 0.133: 75 0.133 - 0.177: 14 0.177 - 0.222: 8 Chirality restraints: 1119 Sorted by residual: chirality pdb=" CA VAL A 256 " pdb=" N VAL A 256 " pdb=" C VAL A 256 " pdb=" CB VAL A 256 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+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 2.65 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA LEU B 7 " pdb=" N LEU B 7 " pdb=" C LEU B 7 " pdb=" CB LEU B 7 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1116 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 17 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.53e+00 pdb=" C LYS A 17 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS A 17 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA A 18 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 53 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.73e+00 pdb=" C LYS A 53 " 0.038 2.00e-02 2.50e+03 pdb=" O LYS A 53 " -0.014 2.00e-02 2.50e+03 pdb=" N SER A 54 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 7 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" C LEU B 7 " 0.036 2.00e-02 2.50e+03 pdb=" O LEU B 7 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG B 8 " -0.012 2.00e-02 2.50e+03 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 802 2.75 - 3.29: 6440 3.29 - 3.83: 10446 3.83 - 4.36: 11518 4.36 - 4.90: 21289 Nonbonded interactions: 50495 Sorted by model distance: nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.218 2.440 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.242 2.440 nonbonded pdb=" OH TYR R 326 " pdb=" O HOH R 601 " model vdw 2.350 2.440 nonbonded pdb=" OD1 ASN A 292 " pdb=" N LYS A 293 " model vdw 2.352 2.520 nonbonded pdb=" OD1 ASP A 295 " pdb=" N LEU A 296 " model vdw 2.352 2.520 ... (remaining 50490 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 7.740 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 23.030 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6831 Z= 0.304 Angle : 0.766 11.509 9348 Z= 0.506 Chirality : 0.049 0.222 1119 Planarity : 0.004 0.051 1172 Dihedral : 13.493 158.212 2208 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.33 % Allowed : 0.99 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.29), residues: 902 helix: 2.20 (0.27), residues: 397 sheet: 0.32 (0.42), residues: 166 loop : -0.87 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 105 HIS 0.008 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.007 0.001 TYR B 59 ARG 0.004 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 0.749 Fit side-chains REVERT: B 78 LYS cc_start: 0.8439 (ttmm) cc_final: 0.8173 (mttp) REVERT: G 38 MET cc_start: 0.8235 (tpp) cc_final: 0.7914 (mtp) outliers start: 2 outliers final: 1 residues processed: 111 average time/residue: 0.2052 time to fit residues: 29.7573 Evaluate side-chains 88 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 269 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6831 Z= 0.207 Angle : 0.493 7.657 9348 Z= 0.265 Chirality : 0.041 0.151 1119 Planarity : 0.003 0.038 1172 Dihedral : 7.488 147.780 1007 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.49 % Allowed : 8.70 % Favored : 90.80 % 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: 1.19 (0.29), residues: 902 helix: 2.31 (0.27), residues: 400 sheet: 0.31 (0.43), residues: 161 loop : -0.85 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.006 0.001 HIS A 220 PHE 0.012 0.001 PHE B 241 TYR 0.011 0.001 TYR R 308 ARG 0.002 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.699 Fit side-chains REVERT: G 38 MET cc_start: 0.8197 (tpp) cc_final: 0.7846 (mtp) outliers start: 3 outliers final: 3 residues processed: 92 average time/residue: 0.1920 time to fit residues: 23.4108 Evaluate side-chains 90 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 79 optimal weight: 0.0670 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6831 Z= 0.153 Angle : 0.434 6.228 9348 Z= 0.235 Chirality : 0.039 0.145 1119 Planarity : 0.003 0.037 1172 Dihedral : 7.204 149.084 1005 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.66 % Allowed : 11.66 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.29), residues: 902 helix: 2.53 (0.27), residues: 400 sheet: 0.23 (0.42), residues: 163 loop : -0.75 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.006 0.001 HIS A 220 PHE 0.011 0.001 PHE B 241 TYR 0.010 0.001 TYR R 308 ARG 0.001 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.764 Fit side-chains REVERT: G 38 MET cc_start: 0.8168 (tpp) cc_final: 0.7832 (mtp) outliers start: 4 outliers final: 3 residues processed: 99 average time/residue: 0.2083 time to fit residues: 27.3163 Evaluate side-chains 93 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 30.0000 chunk 71 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 6831 Z= 0.375 Angle : 0.555 6.348 9348 Z= 0.300 Chirality : 0.043 0.155 1119 Planarity : 0.004 0.042 1172 Dihedral : 7.501 144.677 1005 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.48 % Allowed : 11.66 % Favored : 86.86 % 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: 0.96 (0.29), residues: 902 helix: 2.05 (0.26), residues: 411 sheet: 0.04 (0.42), residues: 163 loop : -0.87 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.008 0.001 HIS A 357 PHE 0.020 0.002 PHE B 241 TYR 0.017 0.001 TYR R 308 ARG 0.004 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.772 Fit side-chains REVERT: A 211 LYS cc_start: 0.8176 (mptt) cc_final: 0.7906 (mmtt) REVERT: G 38 MET cc_start: 0.8238 (tpp) cc_final: 0.7831 (mtp) REVERT: R 231 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8278 (tm-30) outliers start: 9 outliers final: 7 residues processed: 94 average time/residue: 0.1983 time to fit residues: 24.8249 Evaluate side-chains 90 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 0.0370 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 overall best weight: 1.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6831 Z= 0.217 Angle : 0.470 6.219 9348 Z= 0.255 Chirality : 0.040 0.147 1119 Planarity : 0.003 0.041 1172 Dihedral : 7.268 144.867 1005 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.97 % Allowed : 12.81 % Favored : 85.22 % 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: 0.99 (0.29), residues: 902 helix: 2.14 (0.27), residues: 409 sheet: -0.05 (0.42), residues: 163 loop : -0.87 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.008 0.001 HIS A 220 PHE 0.014 0.001 PHE B 241 TYR 0.012 0.001 TYR A 339 ARG 0.002 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.710 Fit side-chains REVERT: A 235 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8227 (tt) REVERT: B 188 MET cc_start: 0.9120 (mmm) cc_final: 0.8440 (mmt) REVERT: B 234 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7354 (t80) REVERT: G 38 MET cc_start: 0.8148 (tpp) cc_final: 0.7739 (mtp) REVERT: R 231 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8198 (tm-30) outliers start: 12 outliers final: 7 residues processed: 92 average time/residue: 0.2163 time to fit residues: 25.9472 Evaluate side-chains 91 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE 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 G residue 25 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.5980 chunk 21 optimal weight: 0.0770 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6831 Z= 0.135 Angle : 0.431 6.281 9348 Z= 0.233 Chirality : 0.039 0.141 1119 Planarity : 0.003 0.039 1172 Dihedral : 7.080 146.494 1005 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.31 % Allowed : 13.96 % Favored : 84.73 % 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: 1.22 (0.29), residues: 902 helix: 2.48 (0.27), residues: 400 sheet: 0.08 (0.42), residues: 161 loop : -0.88 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 297 HIS 0.008 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.750 Fit side-chains REVERT: B 188 MET cc_start: 0.9140 (mmm) cc_final: 0.8507 (mmt) REVERT: B 234 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7133 (t80) REVERT: G 38 MET cc_start: 0.8173 (tpp) cc_final: 0.7790 (mtp) REVERT: R 231 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8183 (tm-30) outliers start: 8 outliers final: 5 residues processed: 92 average time/residue: 0.2055 time to fit residues: 25.2659 Evaluate side-chains 92 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6831 Z= 0.179 Angle : 0.446 6.333 9348 Z= 0.241 Chirality : 0.039 0.142 1119 Planarity : 0.003 0.039 1172 Dihedral : 7.096 146.162 1005 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.31 % Allowed : 14.45 % Favored : 84.24 % 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: 1.18 (0.29), residues: 902 helix: 2.41 (0.27), residues: 404 sheet: 0.01 (0.42), residues: 163 loop : -0.86 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.008 0.001 HIS A 220 PHE 0.012 0.001 PHE B 241 TYR 0.011 0.001 TYR R 308 ARG 0.001 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.760 Fit side-chains REVERT: B 234 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7167 (t80) REVERT: G 38 MET cc_start: 0.8179 (tpp) cc_final: 0.7786 (mtp) REVERT: R 231 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8212 (tm-30) outliers start: 8 outliers final: 7 residues processed: 93 average time/residue: 0.1971 time to fit residues: 24.3739 Evaluate side-chains 93 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 G residue 25 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.0770 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 78 optimal weight: 0.3980 chunk 82 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 0.0470 chunk 48 optimal weight: 0.5980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6831 Z= 0.111 Angle : 0.412 6.304 9348 Z= 0.222 Chirality : 0.038 0.134 1119 Planarity : 0.003 0.037 1172 Dihedral : 6.941 147.560 1005 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.15 % Allowed : 14.94 % Favored : 83.91 % 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: 1.42 (0.29), residues: 902 helix: 2.59 (0.27), residues: 401 sheet: 0.19 (0.43), residues: 159 loop : -0.70 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 105 HIS 0.007 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.008 0.001 TYR R 308 ARG 0.001 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.712 Fit side-chains REVERT: B 234 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7107 (t80) REVERT: G 38 MET cc_start: 0.8200 (tpp) cc_final: 0.7857 (mtp) REVERT: R 231 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8129 (tm-30) outliers start: 7 outliers final: 5 residues processed: 96 average time/residue: 0.1882 time to fit residues: 23.9903 Evaluate side-chains 93 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 79 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6831 Z= 0.149 Angle : 0.429 6.383 9348 Z= 0.231 Chirality : 0.039 0.136 1119 Planarity : 0.003 0.038 1172 Dihedral : 6.976 147.220 1005 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.99 % Allowed : 15.76 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.29), residues: 902 helix: 2.61 (0.27), residues: 401 sheet: 0.13 (0.42), residues: 163 loop : -0.68 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE B 241 TYR 0.010 0.001 TYR R 308 ARG 0.001 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.736 Fit side-chains REVERT: B 234 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7143 (t80) REVERT: G 38 MET cc_start: 0.8224 (tpp) cc_final: 0.7868 (mtp) REVERT: R 231 GLN cc_start: 0.8447 (tm-30) cc_final: 0.8162 (tm-30) outliers start: 6 outliers final: 5 residues processed: 90 average time/residue: 0.1961 time to fit residues: 23.3313 Evaluate side-chains 90 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 0.0980 chunk 7 optimal weight: 2.9990 chunk 54 optimal weight: 0.0970 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6831 Z= 0.116 Angle : 0.413 6.353 9348 Z= 0.221 Chirality : 0.039 0.132 1119 Planarity : 0.003 0.037 1172 Dihedral : 6.910 147.532 1005 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.99 % Allowed : 15.60 % Favored : 83.42 % 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: 1.51 (0.29), residues: 902 helix: 2.67 (0.27), residues: 401 sheet: 0.15 (0.42), residues: 166 loop : -0.64 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 105 HIS 0.004 0.001 HIS A 220 PHE 0.011 0.001 PHE A 212 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG A 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.737 Fit side-chains REVERT: B 234 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7038 (t80) REVERT: G 38 MET cc_start: 0.8205 (tpp) cc_final: 0.7862 (mtp) REVERT: R 231 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8162 (tm-30) outliers start: 6 outliers final: 5 residues processed: 90 average time/residue: 0.2077 time to fit residues: 24.7780 Evaluate side-chains 92 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.0270 chunk 70 optimal weight: 0.0980 chunk 29 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.127029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.099777 restraints weight = 33238.781| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 4.58 r_work: 0.3099 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6831 Z= 0.126 Angle : 0.419 6.394 9348 Z= 0.224 Chirality : 0.039 0.132 1119 Planarity : 0.003 0.038 1172 Dihedral : 6.902 147.467 1005 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.99 % Allowed : 15.93 % Favored : 83.09 % 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 (0.29), residues: 902 helix: 2.72 (0.27), residues: 401 sheet: 0.24 (0.43), residues: 159 loop : -0.68 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 339 HIS 0.004 0.001 HIS A 357 PHE 0.010 0.001 PHE A 212 TYR 0.009 0.001 TYR R 308 ARG 0.002 0.000 ARG R 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1806.08 seconds wall clock time: 34 minutes 14.22 seconds (2054.22 seconds total)