Starting phenix.real_space_refine on Wed Sep 17 23:34:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8q_44352/09_2025/9b8q_44352.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8q_44352/09_2025/9b8q_44352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b8q_44352/09_2025/9b8q_44352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8q_44352/09_2025/9b8q_44352.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8q_44352/09_2025/9b8q_44352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8q_44352/09_2025/9b8q_44352.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 7579 2.51 5 N 2356 2.21 5 O 2368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12348 Number of models: 1 Model: "" Number of chains: 9 Chain: "G" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2155 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 260} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 363} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 912 Unresolved non-hydrogen angles: 1152 Unresolved non-hydrogen dihedrals: 752 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'GLU:plan': 21, 'PHE:plan': 7, 'TRP:plan': 3, 'GLN:plan1': 14, 'HIS:plan': 5, 'ASN:plan1': 20, 'TYR:plan': 9, 'ASP:plan': 22, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 478 Chain: "I" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1087 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 1, 'TRANS': 146} Chain breaks: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "J" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1171 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 147} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "K" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 914 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 10, 'ASN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 111 Chain: "M" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 740 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'TRANS': 101} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 52 Chain: "N" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 825 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 104} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "O" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 625 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'TRANS': 102} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 13, 'GLU:plan': 9, 'ARG:plan': 8, 'ASP:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 144 Chain: "T" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 2136 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 388} Link IDs: {'PTRANS': 8, 'TRANS': 421} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1462 Unresolved non-hydrogen angles: 1859 Unresolved non-hydrogen dihedrals: 1236 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLU:plan': 38, 'ARG:plan': 22, 'ASN:plan1': 19, 'TRP:plan': 8, 'GLN:plan1': 34, 'TYR:plan': 17, 'ASP:plan': 19, 'PHE:plan': 17, 'HIS:plan': 11} Unresolved non-hydrogen planarities: 860 Chain: "a" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2695 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 3.21, per 1000 atoms: 0.26 Number of scatterers: 12348 At special positions: 0 Unit cell: (156.56, 175.1, 188.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 2368 8.00 N 2356 7.00 C 7579 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.24 Conformation dependent library (CDL) restraints added in 616.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3644 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 79.1% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'G' and resid 14 through 30 removed outlier: 3.860A pdb=" N THR G 18 " --> pdb=" O THR G 14 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LYS G 21 " --> pdb=" O GLN G 17 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 80 removed outlier: 3.704A pdb=" N ALA G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 84 removed outlier: 3.881A pdb=" N LYS G 84 " --> pdb=" O GLU G 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 81 through 84' Processing helix chain 'G' and resid 97 through 104 Processing helix chain 'G' and resid 117 through 158 removed outlier: 3.525A pdb=" N ILE G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY G 128 " --> pdb=" O ILE G 124 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA G 140 " --> pdb=" O LEU G 136 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER G 141 " --> pdb=" O LYS G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 170 removed outlier: 3.503A pdb=" N VAL G 170 " --> pdb=" O ALA G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 203 Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 254 through 310 removed outlier: 4.177A pdb=" N GLY G 277 " --> pdb=" O LYS G 273 " (cutoff:3.500A) Proline residue: G 278 - end of helix removed outlier: 3.848A pdb=" N SER G 288 " --> pdb=" O LYS G 284 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU G 289 " --> pdb=" O VAL G 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 339 Processing helix chain 'I' and resid 4 through 108 removed outlier: 3.641A pdb=" N LYS I 52 " --> pdb=" O THR I 48 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS I 107 " --> pdb=" O SER I 103 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP I 108 " --> pdb=" O LYS I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 119 Processing helix chain 'I' and resid 195 through 216 removed outlier: 3.511A pdb=" N GLN I 206 " --> pdb=" O LEU I 202 " (cutoff:3.500A) Proline residue: I 209 - end of helix Processing helix chain 'J' and resid 5 through 106 Processing helix chain 'J' and resid 108 through 122 removed outlier: 3.751A pdb=" N VAL J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 217 removed outlier: 4.097A pdb=" N ASP J 201 " --> pdb=" O GLU J 197 " (cutoff:3.500A) Proline residue: J 209 - end of helix Processing helix chain 'K' and resid 4 through 105 removed outlier: 3.632A pdb=" N GLN K 11 " --> pdb=" O ASP K 7 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE K 38 " --> pdb=" O ALA K 34 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS K 104 " --> pdb=" O GLN K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 217 removed outlier: 3.692A pdb=" N GLN K 206 " --> pdb=" O LEU K 202 " (cutoff:3.500A) Proline residue: K 209 - end of helix Processing helix chain 'M' and resid 4 through 62 removed outlier: 3.955A pdb=" N LYS M 34 " --> pdb=" O ALA M 30 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLN M 41 " --> pdb=" O LYS M 37 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N MET M 42 " --> pdb=" O GLU M 38 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU M 43 " --> pdb=" O GLU M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 104 removed outlier: 3.973A pdb=" N ASN M 68 " --> pdb=" O GLY M 64 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLU M 93 " --> pdb=" O GLN M 89 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ARG M 94 " --> pdb=" O ARG M 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 105 removed outlier: 3.545A pdb=" N ALA N 25 " --> pdb=" O LYS N 21 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG N 90 " --> pdb=" O SER N 86 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN N 91 " --> pdb=" O SER N 87 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLU N 93 " --> pdb=" O GLN N 89 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ARG N 94 " --> pdb=" O ARG N 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 105 removed outlier: 3.665A pdb=" N ALA O 14 " --> pdb=" O GLN O 10 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL O 22 " --> pdb=" O ALA O 18 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU O 69 " --> pdb=" O SER O 65 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN O 91 " --> pdb=" O SER O 87 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU O 93 " --> pdb=" O GLN O 89 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ARG O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 29 Processing helix chain 'T' and resid 33 through 39 removed outlier: 3.757A pdb=" N LEU T 37 " --> pdb=" O TRP T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 56 Processing helix chain 'T' and resid 58 through 69 Processing helix chain 'T' and resid 69 through 84 removed outlier: 3.997A pdb=" N ALA T 74 " --> pdb=" O GLY T 70 " (cutoff:3.500A) Processing helix chain 'T' and resid 86 through 104 removed outlier: 3.801A pdb=" N VAL T 90 " --> pdb=" O LYS T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 107 through 119 removed outlier: 3.941A pdb=" N PHE T 111 " --> pdb=" O ARG T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 132 Processing helix chain 'T' and resid 134 through 152 Processing helix chain 'T' and resid 158 through 174 Processing helix chain 'T' and resid 193 through 210 Processing helix chain 'T' and resid 211 through 221 removed outlier: 3.661A pdb=" N ARG T 215 " --> pdb=" O VAL T 211 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE T 216 " --> pdb=" O ASN T 212 " (cutoff:3.500A) Processing helix chain 'T' and resid 222 through 233 Processing helix chain 'T' and resid 236 through 251 Processing helix chain 'T' and resid 253 through 260 Processing helix chain 'T' and resid 261 through 263 No H-bonds generated for 'chain 'T' and resid 261 through 263' Processing helix chain 'T' and resid 264 through 276 removed outlier: 4.438A pdb=" N VAL T 268 " --> pdb=" O ASN T 264 " (cutoff:3.500A) Processing helix chain 'T' and resid 278 through 295 Processing helix chain 'T' and resid 298 through 312 Processing helix chain 'T' and resid 313 through 324 removed outlier: 3.949A pdb=" N GLN T 317 " --> pdb=" O LYS T 313 " (cutoff:3.500A) Processing helix chain 'T' and resid 328 through 350 removed outlier: 3.628A pdb=" N SER T 332 " --> pdb=" O ASP T 328 " (cutoff:3.500A) Processing helix chain 'T' and resid 351 through 362 Processing helix chain 'T' and resid 367 through 371 Processing helix chain 'T' and resid 372 through 380 Processing helix chain 'T' and resid 381 through 383 No H-bonds generated for 'chain 'T' and resid 381 through 383' Processing helix chain 'T' and resid 384 through 401 removed outlier: 5.135A pdb=" N LEU T 390 " --> pdb=" O LYS T 386 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU T 391 " --> pdb=" O ASN T 387 " (cutoff:3.500A) Processing helix chain 'T' and resid 403 through 421 Processing helix chain 'T' and resid 423 through 432 removed outlier: 4.529A pdb=" N VAL T 427 " --> pdb=" O ARG T 423 " (cutoff:3.500A) Processing helix chain 'T' and resid 432 through 442 removed outlier: 4.049A pdb=" N HIS T 442 " --> pdb=" O MET T 438 " (cutoff:3.500A) Processing helix chain 'T' and resid 445 through 460 removed outlier: 3.554A pdb=" N ASN T 451 " --> pdb=" O GLN T 447 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 33 removed outlier: 4.071A pdb=" N TYR a 23 " --> pdb=" O SER a 19 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N CYS a 24 " --> pdb=" O GLU a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 50 removed outlier: 7.841A pdb=" N LYS a 50 " --> pdb=" O PHE a 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 75 Processing helix chain 'a' and resid 92 through 139 removed outlier: 4.398A pdb=" N ASP a 96 " --> pdb=" O ARG a 92 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU a 108 " --> pdb=" O ILE a 104 " (cutoff:3.500A) Processing helix chain 'a' and resid 179 through 191 Processing helix chain 'a' and resid 226 through 240 Processing helix chain 'a' and resid 250 through 309 removed outlier: 3.676A pdb=" N ASN a 289 " --> pdb=" O ALA a 285 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ARG a 291 " --> pdb=" O ALA a 287 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL a 292 " --> pdb=" O LYS a 288 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU a 309 " --> pdb=" O HIS a 305 " (cutoff:3.500A) Processing helix chain 'a' and resid 329 through 345 Processing sheet with id=AA1, first strand: chain 'G' and resid 33 through 37 Processing sheet with id=AA2, first strand: chain 'G' and resid 182 through 185 removed outlier: 6.498A pdb=" N ASN G 226 " --> pdb=" O VAL G 215 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL G 215 " --> pdb=" O ASN G 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 36 through 37 Processing sheet with id=AA4, first strand: chain 'a' and resid 169 through 176 removed outlier: 7.891A pdb=" N VAL a 215 " --> pdb=" O ASN a 204 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ASN a 204 " --> pdb=" O VAL a 215 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS a 217 " --> pdb=" O ILE a 202 " (cutoff:3.500A) 1225 hydrogen bonds defined for protein. 3636 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4551 1.34 - 1.46: 1413 1.46 - 1.57: 6381 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 12423 Sorted by residual: bond pdb=" C ARG O 17 " pdb=" N ALA O 18 " ideal model delta sigma weight residual 1.335 1.559 -0.224 1.31e-02 5.83e+03 2.91e+02 bond pdb=" CA PHE G 316 " pdb=" C PHE G 316 " ideal model delta sigma weight residual 1.530 1.510 0.020 1.23e-02 6.61e+03 2.68e+00 bond pdb=" CA ILE T 266 " pdb=" CB ILE T 266 " ideal model delta sigma weight residual 1.537 1.521 0.017 1.29e-02 6.01e+03 1.66e+00 bond pdb=" CB PHE G 316 " pdb=" CG PHE G 316 " ideal model delta sigma weight residual 1.502 1.473 0.029 2.30e-02 1.89e+03 1.61e+00 bond pdb=" CB LEU G 300 " pdb=" CG LEU G 300 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.57e+00 ... (remaining 12418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 16404 1.57 - 3.14: 436 3.14 - 4.71: 52 4.71 - 6.28: 6 6.28 - 7.85: 2 Bond angle restraints: 16900 Sorted by residual: angle pdb=" C ARG O 17 " pdb=" N ALA O 18 " pdb=" CA ALA O 18 " ideal model delta sigma weight residual 120.28 126.58 -6.30 1.34e+00 5.57e-01 2.21e+01 angle pdb=" C LEU G 54 " pdb=" N SER G 55 " pdb=" CA SER G 55 " ideal model delta sigma weight residual 121.18 116.17 5.01 1.98e+00 2.55e-01 6.41e+00 angle pdb=" CA VAL T 277 " pdb=" C VAL T 277 " pdb=" N LYS T 278 " ideal model delta sigma weight residual 116.60 120.12 -3.52 1.45e+00 4.76e-01 5.88e+00 angle pdb=" N THR G 103 " pdb=" CA THR G 103 " pdb=" CB THR G 103 " ideal model delta sigma weight residual 110.22 113.88 -3.66 1.54e+00 4.22e-01 5.63e+00 angle pdb=" N VAL a 323 " pdb=" CA VAL a 323 " pdb=" C VAL a 323 " ideal model delta sigma weight residual 108.06 111.03 -2.97 1.28e+00 6.10e-01 5.39e+00 ... (remaining 16895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6806 17.90 - 35.81: 636 35.81 - 53.71: 154 53.71 - 71.61: 34 71.61 - 89.52: 15 Dihedral angle restraints: 7645 sinusoidal: 2111 harmonic: 5534 Sorted by residual: dihedral pdb=" CA VAL a 323 " pdb=" C VAL a 323 " pdb=" N TRP a 324 " pdb=" CA TRP a 324 " ideal model delta harmonic sigma weight residual 180.00 157.82 22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA CYS a 191 " pdb=" C CYS a 191 " pdb=" N ARG a 192 " pdb=" CA ARG a 192 " ideal model delta harmonic sigma weight residual -180.00 -158.70 -21.30 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA LEU G 58 " pdb=" C LEU G 58 " pdb=" N ALA G 59 " pdb=" CA ALA G 59 " ideal model delta harmonic sigma weight residual 180.00 161.35 18.65 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 7642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1465 0.032 - 0.064: 418 0.064 - 0.095: 140 0.095 - 0.127: 33 0.127 - 0.159: 9 Chirality restraints: 2065 Sorted by residual: chirality pdb=" CA ILE a 221 " pdb=" N ILE a 221 " pdb=" C ILE a 221 " pdb=" CB ILE a 221 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CA ILE a 320 " pdb=" N ILE a 320 " pdb=" C ILE a 320 " pdb=" CB ILE a 320 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.12e-01 chirality pdb=" CB THR M 77 " pdb=" CA THR M 77 " pdb=" OG1 THR M 77 " pdb=" CG2 THR M 77 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 2062 not shown) Planarity restraints: 2306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 104 " -0.252 9.50e-02 1.11e+02 1.13e-01 8.81e+00 pdb=" NE ARG G 104 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG G 104 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG G 104 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG G 104 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG N 107 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO N 108 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO N 108 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO N 108 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG a 66 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C ARG a 66 " 0.028 2.00e-02 2.50e+03 pdb=" O ARG a 66 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE a 67 " -0.009 2.00e-02 2.50e+03 ... (remaining 2303 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 127 2.61 - 3.18: 12207 3.18 - 3.75: 19957 3.75 - 4.33: 22017 4.33 - 4.90: 37332 Nonbonded interactions: 91640 Sorted by model distance: nonbonded pdb=" O LEU J 215 " pdb=" OG SER N 87 " model vdw 2.034 3.040 nonbonded pdb=" O THR J 195 " pdb=" OG SER J 198 " model vdw 2.042 3.040 nonbonded pdb=" OH TYR K 57 " pdb=" O ARG O 48 " model vdw 2.049 3.040 nonbonded pdb=" O ASP a 329 " pdb=" OG SER a 332 " model vdw 2.154 3.040 nonbonded pdb=" OE1 GLN a 316 " pdb=" N LYS a 317 " model vdw 2.154 3.120 ... (remaining 91635 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'I' and ((resid 4 through 42 and (name N or name CA or name C or name O o \ r name CB )) or resid 43 or (resid 44 through 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 through 105 or resid 118 or resid 193 thro \ ugh 221)) selection = (chain 'J' and ((resid 4 through 42 and (name N or name CA or name C or name O o \ r name CB )) or resid 43 or (resid 44 through 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 through 96 or (resid 97 through 105 and (n \ ame N or name CA or name C or name O or name CB )) or resid 118 or resid 193 thr \ ough 221)) selection = (chain 'K' and (resid 4 through 105 or resid 180 or resid 193 through 221)) } ncs_group { reference = (chain 'M' and ((resid 4 through 63 and (name N or name CA or name C or name O o \ r name CB )) or resid 64 through 104)) selection = (chain 'N' and ((resid 4 through 63 and (name N or name CA or name C or name O o \ r name CB )) or resid 64 through 104)) selection = (chain 'O' and ((resid 4 through 72 and (name N or name CA or name C or name O o \ r name CB )) or resid 73 through 104)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.850 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.660 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 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 : 0.005 0.224 12423 Z= 0.281 Angle : 0.616 7.852 16900 Z= 0.371 Chirality : 0.036 0.159 2065 Planarity : 0.005 0.113 2306 Dihedral : 16.286 89.518 4001 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.26 % Favored : 95.69 % Rotamer: Outliers : 3.66 % Allowed : 25.24 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.20), residues: 1856 helix: 2.25 (0.13), residues: 1420 sheet: 0.52 (0.56), residues: 93 loop : -1.51 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 104 TYR 0.012 0.001 TYR I 57 PHE 0.020 0.002 PHE a 196 TRP 0.013 0.002 TRP a 324 HIS 0.003 0.001 HIS a 305 Details of bonding type rmsd covalent geometry : bond 0.00506 (12423) covalent geometry : angle 0.61572 (16900) hydrogen bonds : bond 0.09427 ( 1225) hydrogen bonds : angle 5.11541 ( 3636) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 221 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 301 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.6668 (ttt180) REVERT: G 306 SER cc_start: 0.6361 (p) cc_final: 0.5744 (p) REVERT: I 26 LYS cc_start: 0.8447 (mmmt) cc_final: 0.7656 (tppt) REVERT: I 37 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7658 (tp30) REVERT: I 54 MET cc_start: 0.8014 (mmm) cc_final: 0.7298 (mmm) REVERT: J 54 MET cc_start: 0.7544 (mtt) cc_final: 0.7289 (mtt) REVERT: J 197 GLU cc_start: 0.7831 (mp0) cc_final: 0.7451 (mt-10) REVERT: K 66 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7315 (tt0) REVERT: K 76 MET cc_start: 0.8000 (mmt) cc_final: 0.7585 (tpp) REVERT: K 212 ARG cc_start: 0.7996 (ttt-90) cc_final: 0.6972 (ttm170) REVERT: M 42 MET cc_start: 0.8054 (mmm) cc_final: 0.7463 (tmm) REVERT: M 84 MET cc_start: 0.6463 (mtt) cc_final: 0.6212 (mtt) outliers start: 30 outliers final: 22 residues processed: 238 average time/residue: 0.1138 time to fit residues: 37.9884 Evaluate side-chains 225 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 301 ARG Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 205 GLN Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 52 GLU Chi-restraints excluded: chain N residue 88 GLN Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 261 VAL Chi-restraints excluded: chain a residue 303 ILE Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 351 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.0050 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 71 GLN O 91 ASN a 14 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.178667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.154865 restraints weight = 29433.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.153218 restraints weight = 19199.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.154462 restraints weight = 18675.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.154604 restraints weight = 12349.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.155067 restraints weight = 10946.828| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12423 Z= 0.143 Angle : 0.515 9.092 16900 Z= 0.280 Chirality : 0.036 0.158 2065 Planarity : 0.003 0.038 2306 Dihedral : 5.598 75.671 2017 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.26 % Favored : 97.68 % Rotamer: Outliers : 5.24 % Allowed : 21.95 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.36 (0.20), residues: 1856 helix: 3.03 (0.13), residues: 1427 sheet: 0.57 (0.57), residues: 89 loop : -1.10 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 38 TYR 0.017 0.002 TYR a 245 PHE 0.045 0.002 PHE G 316 TRP 0.008 0.002 TRP a 324 HIS 0.002 0.000 HIS a 343 Details of bonding type rmsd covalent geometry : bond 0.00302 (12423) covalent geometry : angle 0.51510 (16900) hydrogen bonds : bond 0.03873 ( 1225) hydrogen bonds : angle 3.76785 ( 3636) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 26 LYS cc_start: 0.8185 (mmmt) cc_final: 0.7272 (tppt) REVERT: I 37 GLU cc_start: 0.8496 (mm-30) cc_final: 0.7912 (tp30) REVERT: I 54 MET cc_start: 0.8384 (mmm) cc_final: 0.7596 (mmm) REVERT: I 62 LYS cc_start: 0.9230 (tppt) cc_final: 0.8767 (ttmt) REVERT: J 207 MET cc_start: 0.7082 (mmm) cc_final: 0.6864 (ttt) REVERT: K 66 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7086 (tt0) REVERT: K 76 MET cc_start: 0.7859 (mmt) cc_final: 0.7420 (tpp) REVERT: K 212 ARG cc_start: 0.7736 (ttt-90) cc_final: 0.5855 (mtt180) REVERT: M 42 MET cc_start: 0.8046 (mmm) cc_final: 0.7493 (tpt) REVERT: M 50 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8074 (tp30) REVERT: N 88 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7552 (pp30) REVERT: a 12 LEU cc_start: 0.8319 (mt) cc_final: 0.8068 (mt) REVERT: a 209 PRO cc_start: 0.9014 (Cg_endo) cc_final: 0.8789 (Cg_exo) REVERT: a 243 SER cc_start: 0.7308 (m) cc_final: 0.6950 (t) REVERT: a 338 ARG cc_start: 0.8514 (tpp80) cc_final: 0.7968 (mmm-85) outliers start: 43 outliers final: 20 residues processed: 249 average time/residue: 0.1081 time to fit residues: 38.5235 Evaluate side-chains 223 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 58 CYS Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 113 THR Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 341 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 78 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 103 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 101 optimal weight: 30.0000 chunk 63 optimal weight: 0.9990 chunk 8 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 63 GLN N 53 GLN a 14 GLN a 225 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.179636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.155882 restraints weight = 29723.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.154434 restraints weight = 18927.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.155540 restraints weight = 16814.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.155942 restraints weight = 11335.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.156235 restraints weight = 10391.711| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12423 Z= 0.120 Angle : 0.457 8.610 16900 Z= 0.249 Chirality : 0.034 0.153 2065 Planarity : 0.003 0.030 2306 Dihedral : 3.898 53.809 1980 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.37 % Favored : 97.58 % Rotamer: Outliers : 4.51 % Allowed : 24.76 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.74 (0.20), residues: 1856 helix: 3.30 (0.13), residues: 1431 sheet: 0.59 (0.59), residues: 87 loop : -0.98 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 309 TYR 0.012 0.001 TYR I 57 PHE 0.028 0.002 PHE a 335 TRP 0.010 0.001 TRP a 324 HIS 0.001 0.001 HIS G 296 Details of bonding type rmsd covalent geometry : bond 0.00247 (12423) covalent geometry : angle 0.45680 (16900) hydrogen bonds : bond 0.03568 ( 1225) hydrogen bonds : angle 3.50089 ( 3636) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 227 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 317 GLN cc_start: 0.8065 (mp10) cc_final: 0.7830 (pm20) REVERT: I 26 LYS cc_start: 0.8055 (mmmt) cc_final: 0.7316 (tppt) REVERT: I 37 GLU cc_start: 0.8497 (mm-30) cc_final: 0.7877 (tp30) REVERT: I 42 LYS cc_start: 0.8555 (ttpp) cc_final: 0.8109 (ttmm) REVERT: I 54 MET cc_start: 0.8316 (mmm) cc_final: 0.7567 (mmm) REVERT: I 62 LYS cc_start: 0.9241 (tppt) cc_final: 0.8838 (ttmt) REVERT: J 42 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7803 (ttmm) REVERT: K 66 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7099 (tt0) REVERT: K 76 MET cc_start: 0.7824 (mmt) cc_final: 0.7331 (tpp) REVERT: K 212 ARG cc_start: 0.7797 (ttt-90) cc_final: 0.5743 (mtt180) REVERT: M 39 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7717 (tm-30) REVERT: M 42 MET cc_start: 0.7943 (mmm) cc_final: 0.7305 (tpt) REVERT: M 50 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8138 (tp30) REVERT: N 85 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7774 (tm-30) REVERT: N 88 GLN cc_start: 0.8035 (tm-30) cc_final: 0.7338 (pp30) REVERT: a 209 PRO cc_start: 0.9054 (Cg_endo) cc_final: 0.8826 (Cg_exo) outliers start: 37 outliers final: 22 residues processed: 247 average time/residue: 0.1155 time to fit residues: 40.6885 Evaluate side-chains 226 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 113 THR Chi-restraints excluded: chain a residue 130 PHE Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 218 SER Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 256 GLU Chi-restraints excluded: chain a residue 268 LEU Chi-restraints excluded: chain a residue 351 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 10.0000 chunk 109 optimal weight: 50.0000 chunk 145 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 84 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 63 GLN N 53 GLN a 14 GLN ** a 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.170670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.146979 restraints weight = 29370.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.145804 restraints weight = 20805.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.146561 restraints weight = 20001.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.146854 restraints weight = 12873.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.147312 restraints weight = 11316.352| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12423 Z= 0.284 Angle : 0.661 10.118 16900 Z= 0.353 Chirality : 0.040 0.168 2065 Planarity : 0.004 0.036 2306 Dihedral : 4.220 46.909 1975 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.91 % Favored : 97.04 % Rotamer: Outliers : 7.80 % Allowed : 25.85 % Favored : 66.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.81 (0.19), residues: 1856 helix: 2.64 (0.13), residues: 1430 sheet: 0.75 (0.66), residues: 66 loop : -1.31 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 80 TYR 0.018 0.002 TYR I 57 PHE 0.045 0.003 PHE G 316 TRP 0.010 0.002 TRP a 188 HIS 0.003 0.001 HIS a 305 Details of bonding type rmsd covalent geometry : bond 0.00624 (12423) covalent geometry : angle 0.66061 (16900) hydrogen bonds : bond 0.04260 ( 1225) hydrogen bonds : angle 4.13284 ( 3636) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 206 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 317 GLN cc_start: 0.8283 (mp10) cc_final: 0.7988 (pm20) REVERT: I 26 LYS cc_start: 0.8459 (mmmt) cc_final: 0.7647 (tppt) REVERT: I 37 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7905 (tp30) REVERT: I 42 LYS cc_start: 0.8689 (ttpp) cc_final: 0.8160 (ttmm) REVERT: I 47 GLN cc_start: 0.8820 (tp40) cc_final: 0.8355 (tp40) REVERT: I 54 MET cc_start: 0.8416 (mmm) cc_final: 0.7493 (mmm) REVERT: I 56 TYR cc_start: 0.8793 (t80) cc_final: 0.8434 (t80) REVERT: J 42 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8079 (mtmt) REVERT: J 115 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8279 (tt) REVERT: J 196 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7454 (mt) REVERT: K 66 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7261 (tt0) REVERT: K 76 MET cc_start: 0.8194 (mmt) cc_final: 0.7787 (tpp) REVERT: K 93 ASP cc_start: 0.7949 (t0) cc_final: 0.7745 (t0) REVERT: K 212 ARG cc_start: 0.7864 (ttt-90) cc_final: 0.6465 (ttm170) REVERT: M 39 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7928 (tm-30) REVERT: M 42 MET cc_start: 0.8034 (mmm) cc_final: 0.7676 (tpt) REVERT: M 45 GLU cc_start: 0.8231 (tm-30) cc_final: 0.8028 (tm-30) REVERT: M 50 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8090 (tp30) REVERT: M 96 LEU cc_start: 0.6370 (OUTLIER) cc_final: 0.5942 (tt) REVERT: N 88 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7499 (pp30) REVERT: O 75 GLN cc_start: 0.8979 (tp40) cc_final: 0.8628 (tp-100) REVERT: a 177 ARG cc_start: 0.8099 (mmm-85) cc_final: 0.7757 (mmm-85) REVERT: a 209 PRO cc_start: 0.9110 (Cg_endo) cc_final: 0.8875 (Cg_exo) REVERT: a 243 SER cc_start: 0.7840 (OUTLIER) cc_final: 0.7533 (t) REVERT: a 295 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8447 (tp) outliers start: 64 outliers final: 43 residues processed: 245 average time/residue: 0.1130 time to fit residues: 39.8790 Evaluate side-chains 243 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 194 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain J residue 208 MET Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 87 SER Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 102 MET Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain a residue 96 ASP Chi-restraints excluded: chain a residue 113 THR Chi-restraints excluded: chain a residue 130 PHE Chi-restraints excluded: chain a residue 170 PHE Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 218 SER Chi-restraints excluded: chain a residue 232 ARG Chi-restraints excluded: chain a residue 243 SER Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 256 GLU Chi-restraints excluded: chain a residue 261 VAL Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain a residue 320 ILE Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 341 THR Chi-restraints excluded: chain a residue 348 VAL Chi-restraints excluded: chain a residue 351 ILE Chi-restraints excluded: chain a residue 352 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 40.0000 chunk 138 optimal weight: 20.0000 chunk 45 optimal weight: 0.6980 chunk 11 optimal weight: 0.0040 chunk 92 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 127 optimal weight: 30.0000 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 14 HIS N 53 GLN a 14 GLN a 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.175496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.151320 restraints weight = 29604.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.149987 restraints weight = 18851.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.150902 restraints weight = 17756.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.151316 restraints weight = 11494.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.151723 restraints weight = 10146.181| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12423 Z= 0.126 Angle : 0.489 9.061 16900 Z= 0.262 Chirality : 0.035 0.198 2065 Planarity : 0.003 0.026 2306 Dihedral : 3.672 18.090 1973 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.42 % Favored : 97.52 % Rotamer: Outliers : 6.10 % Allowed : 28.78 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.41 (0.20), residues: 1856 helix: 3.09 (0.13), residues: 1428 sheet: 0.37 (0.61), residues: 76 loop : -1.10 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 87 TYR 0.014 0.001 TYR I 57 PHE 0.022 0.002 PHE G 316 TRP 0.009 0.001 TRP a 293 HIS 0.001 0.000 HIS a 343 Details of bonding type rmsd covalent geometry : bond 0.00265 (12423) covalent geometry : angle 0.48891 (16900) hydrogen bonds : bond 0.03640 ( 1225) hydrogen bonds : angle 3.59070 ( 3636) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 221 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 61 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7841 (tp) REVERT: I 26 LYS cc_start: 0.8094 (mmmt) cc_final: 0.7278 (tppt) REVERT: I 37 GLU cc_start: 0.8561 (mm-30) cc_final: 0.7901 (tp30) REVERT: I 42 LYS cc_start: 0.8554 (ttpp) cc_final: 0.8056 (ttmm) REVERT: I 54 MET cc_start: 0.8464 (mmm) cc_final: 0.7588 (mmm) REVERT: I 62 LYS cc_start: 0.9285 (tppt) cc_final: 0.8870 (ttmt) REVERT: J 16 MET cc_start: 0.7675 (mmm) cc_final: 0.7464 (mmt) REVERT: J 42 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7974 (ttmm) REVERT: J 101 ARG cc_start: 0.8512 (mmm-85) cc_final: 0.8188 (tpp80) REVERT: K 76 MET cc_start: 0.7936 (mmt) cc_final: 0.7459 (tpp) REVERT: K 212 ARG cc_start: 0.7664 (ttt-90) cc_final: 0.6391 (ttm170) REVERT: M 39 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7919 (tm-30) REVERT: M 42 MET cc_start: 0.8039 (mmm) cc_final: 0.7674 (tpt) REVERT: M 50 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8123 (tp30) REVERT: M 96 LEU cc_start: 0.6330 (OUTLIER) cc_final: 0.5841 (tt) REVERT: N 84 MET cc_start: 0.7269 (ttm) cc_final: 0.7056 (ttm) REVERT: N 88 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7368 (pp30) REVERT: a 94 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7545 (tmt) REVERT: a 127 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7978 (tp30) REVERT: a 177 ARG cc_start: 0.7812 (mmm-85) cc_final: 0.6727 (mmm-85) REVERT: a 209 PRO cc_start: 0.9125 (Cg_endo) cc_final: 0.8915 (Cg_exo) outliers start: 50 outliers final: 31 residues processed: 247 average time/residue: 0.1172 time to fit residues: 41.3387 Evaluate side-chains 243 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain J residue 208 MET Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 102 MET Chi-restraints excluded: chain a residue 94 MET Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 130 PHE Chi-restraints excluded: chain a residue 138 PHE Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 218 SER Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 256 GLU Chi-restraints excluded: chain a residue 261 VAL Chi-restraints excluded: chain a residue 341 THR Chi-restraints excluded: chain a residue 348 VAL Chi-restraints excluded: chain a residue 351 ILE Chi-restraints excluded: chain a residue 352 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 13 optimal weight: 20.0000 chunk 125 optimal weight: 5.9990 chunk 4 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 150 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 15 optimal weight: 40.0000 chunk 168 optimal weight: 1.9990 chunk 101 optimal weight: 30.0000 chunk 153 optimal weight: 0.3980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 66 GLN N 53 GLN a 278 HIS ** a 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.175844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.152285 restraints weight = 29310.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.151360 restraints weight = 19359.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.152352 restraints weight = 17044.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.152586 restraints weight = 10916.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.153076 restraints weight = 10043.935| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12423 Z= 0.124 Angle : 0.496 8.953 16900 Z= 0.265 Chirality : 0.035 0.164 2065 Planarity : 0.003 0.027 2306 Dihedral : 3.549 17.742 1973 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.69 % Favored : 97.25 % Rotamer: Outliers : 5.49 % Allowed : 29.63 % Favored : 64.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.66 (0.20), residues: 1856 helix: 3.24 (0.13), residues: 1440 sheet: 0.40 (0.61), residues: 76 loop : -1.01 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 199 TYR 0.017 0.001 TYR I 56 PHE 0.029 0.002 PHE a 335 TRP 0.006 0.001 TRP G 282 HIS 0.001 0.000 HIS G 296 Details of bonding type rmsd covalent geometry : bond 0.00262 (12423) covalent geometry : angle 0.49577 (16900) hydrogen bonds : bond 0.03476 ( 1225) hydrogen bonds : angle 3.47511 ( 3636) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 214 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 61 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7746 (tp) REVERT: G 315 ASN cc_start: 0.8082 (m-40) cc_final: 0.7571 (t0) REVERT: G 317 GLN cc_start: 0.7976 (pm20) cc_final: 0.7255 (pm20) REVERT: I 26 LYS cc_start: 0.8096 (mmmt) cc_final: 0.7262 (tppt) REVERT: I 37 GLU cc_start: 0.8554 (mm-30) cc_final: 0.7859 (tp30) REVERT: I 42 LYS cc_start: 0.8608 (ttpp) cc_final: 0.8023 (ttmm) REVERT: I 54 MET cc_start: 0.8498 (mmm) cc_final: 0.7541 (mmm) REVERT: I 62 LYS cc_start: 0.9258 (tppt) cc_final: 0.8860 (ttmt) REVERT: J 16 MET cc_start: 0.7517 (mmm) cc_final: 0.7304 (mmt) REVERT: J 42 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8062 (ttmm) REVERT: J 44 ARG cc_start: 0.8762 (mmm-85) cc_final: 0.8471 (tmm-80) REVERT: J 63 GLN cc_start: 0.8860 (tm-30) cc_final: 0.8656 (tm-30) REVERT: J 101 ARG cc_start: 0.8472 (mmm-85) cc_final: 0.8140 (tpp80) REVERT: K 76 MET cc_start: 0.7933 (mmt) cc_final: 0.7411 (tpp) REVERT: K 93 ASP cc_start: 0.7865 (t0) cc_final: 0.7659 (t0) REVERT: K 212 ARG cc_start: 0.7741 (ttt-90) cc_final: 0.6371 (ttm170) REVERT: M 39 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7890 (tm-30) REVERT: M 42 MET cc_start: 0.7979 (mmm) cc_final: 0.7533 (tpt) REVERT: M 50 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8245 (tp30) REVERT: M 96 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.5732 (tt) REVERT: N 84 MET cc_start: 0.7281 (ttm) cc_final: 0.6953 (ttm) REVERT: N 88 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7390 (pp30) REVERT: a 28 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8000 (mm-30) outliers start: 45 outliers final: 35 residues processed: 235 average time/residue: 0.1125 time to fit residues: 37.9114 Evaluate side-chains 242 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain J residue 208 MET Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain a residue 96 ASP Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 111 ILE Chi-restraints excluded: chain a residue 130 PHE Chi-restraints excluded: chain a residue 138 PHE Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 218 SER Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 256 GLU Chi-restraints excluded: chain a residue 261 VAL Chi-restraints excluded: chain a residue 268 LEU Chi-restraints excluded: chain a residue 315 THR Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 341 THR Chi-restraints excluded: chain a residue 348 VAL Chi-restraints excluded: chain a residue 351 ILE Chi-restraints excluded: chain a residue 352 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 143 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 0.0670 chunk 89 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 53 GLN ** a 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.174995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.151261 restraints weight = 29236.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.151308 restraints weight = 19085.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.151351 restraints weight = 17134.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.151503 restraints weight = 11606.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.151802 restraints weight = 10139.463| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12423 Z= 0.134 Angle : 0.500 8.629 16900 Z= 0.267 Chirality : 0.035 0.172 2065 Planarity : 0.003 0.033 2306 Dihedral : 3.533 20.254 1973 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.53 % Favored : 97.41 % Rotamer: Outliers : 5.98 % Allowed : 29.76 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.69 (0.20), residues: 1856 helix: 3.25 (0.13), residues: 1440 sheet: 0.21 (0.61), residues: 79 loop : -0.94 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 104 TYR 0.015 0.001 TYR I 56 PHE 0.033 0.002 PHE G 316 TRP 0.010 0.001 TRP G 107 HIS 0.002 0.000 HIS G 296 Details of bonding type rmsd covalent geometry : bond 0.00287 (12423) covalent geometry : angle 0.50042 (16900) hydrogen bonds : bond 0.03460 ( 1225) hydrogen bonds : angle 3.48125 ( 3636) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 212 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 61 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8116 (tp) REVERT: G 315 ASN cc_start: 0.7897 (m-40) cc_final: 0.7465 (t0) REVERT: G 317 GLN cc_start: 0.7979 (pm20) cc_final: 0.7306 (pm20) REVERT: I 26 LYS cc_start: 0.8121 (mmmt) cc_final: 0.7285 (tppt) REVERT: I 54 MET cc_start: 0.8483 (mmm) cc_final: 0.7589 (mmm) REVERT: I 62 LYS cc_start: 0.9245 (tppt) cc_final: 0.8857 (ttmt) REVERT: J 16 MET cc_start: 0.7497 (mmm) cc_final: 0.7281 (mmt) REVERT: J 42 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8063 (ttmm) REVERT: J 44 ARG cc_start: 0.8696 (mmm-85) cc_final: 0.8398 (tmm-80) REVERT: J 63 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8658 (tm-30) REVERT: J 101 ARG cc_start: 0.8440 (mmm-85) cc_final: 0.8100 (tpp80) REVERT: J 215 LEU cc_start: 0.8470 (tp) cc_final: 0.7793 (tp) REVERT: K 76 MET cc_start: 0.7977 (mmt) cc_final: 0.7502 (tpp) REVERT: K 93 ASP cc_start: 0.7901 (t0) cc_final: 0.7686 (t0) REVERT: K 212 ARG cc_start: 0.7664 (ttt-90) cc_final: 0.5511 (mtt180) REVERT: M 42 MET cc_start: 0.7932 (mmm) cc_final: 0.7257 (tpt) REVERT: M 50 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8076 (tp30) REVERT: M 79 ARG cc_start: 0.7851 (tpm170) cc_final: 0.7612 (tpm170) REVERT: M 96 LEU cc_start: 0.6264 (OUTLIER) cc_final: 0.5743 (tt) REVERT: N 84 MET cc_start: 0.7339 (ttm) cc_final: 0.6977 (ttm) REVERT: N 88 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7450 (pp30) REVERT: a 28 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8108 (mm-30) REVERT: a 94 MET cc_start: 0.8175 (ttt) cc_final: 0.7867 (ttp) REVERT: a 295 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8399 (tp) outliers start: 49 outliers final: 39 residues processed: 235 average time/residue: 0.1101 time to fit residues: 37.0471 Evaluate side-chains 246 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain J residue 208 MET Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain a residue 96 ASP Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 111 ILE Chi-restraints excluded: chain a residue 130 PHE Chi-restraints excluded: chain a residue 138 PHE Chi-restraints excluded: chain a residue 170 PHE Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 218 SER Chi-restraints excluded: chain a residue 243 SER Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 256 GLU Chi-restraints excluded: chain a residue 261 VAL Chi-restraints excluded: chain a residue 268 LEU Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain a residue 315 THR Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 341 THR Chi-restraints excluded: chain a residue 348 VAL Chi-restraints excluded: chain a residue 351 ILE Chi-restraints excluded: chain a residue 352 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 82 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 18 optimal weight: 40.0000 chunk 115 optimal weight: 40.0000 chunk 67 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 127 optimal weight: 30.0000 chunk 150 optimal weight: 6.9990 chunk 10 optimal weight: 0.0570 chunk 71 optimal weight: 0.9980 chunk 61 optimal weight: 0.0870 overall best weight: 0.6276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 10 GLN ** a 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.177498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.153751 restraints weight = 29529.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.151674 restraints weight = 19732.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.153054 restraints weight = 16850.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.153370 restraints weight = 11820.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.153684 restraints weight = 11042.691| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12423 Z= 0.112 Angle : 0.488 8.425 16900 Z= 0.259 Chirality : 0.034 0.173 2065 Planarity : 0.003 0.030 2306 Dihedral : 3.376 18.747 1973 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.42 % Favored : 97.52 % Rotamer: Outliers : 4.15 % Allowed : 31.46 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.95 (0.20), residues: 1856 helix: 3.45 (0.13), residues: 1440 sheet: 0.37 (0.62), residues: 77 loop : -0.91 (0.36), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 104 TYR 0.016 0.001 TYR I 56 PHE 0.018 0.002 PHE a 223 TRP 0.009 0.001 TRP a 324 HIS 0.002 0.000 HIS a 216 Details of bonding type rmsd covalent geometry : bond 0.00232 (12423) covalent geometry : angle 0.48812 (16900) hydrogen bonds : bond 0.03234 ( 1225) hydrogen bonds : angle 3.30666 ( 3636) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 61 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7861 (tp) REVERT: G 315 ASN cc_start: 0.7732 (m-40) cc_final: 0.7263 (t0) REVERT: G 317 GLN cc_start: 0.7901 (pm20) cc_final: 0.7212 (pm20) REVERT: I 26 LYS cc_start: 0.8124 (mmmt) cc_final: 0.7288 (tppt) REVERT: I 42 LYS cc_start: 0.8345 (ttpp) cc_final: 0.8039 (ttmm) REVERT: I 54 MET cc_start: 0.8463 (mmm) cc_final: 0.7677 (mmm) REVERT: I 62 LYS cc_start: 0.9245 (tppt) cc_final: 0.8928 (ttmt) REVERT: I 208 MET cc_start: 0.8010 (tpp) cc_final: 0.7656 (mmp) REVERT: J 16 MET cc_start: 0.7469 (mmm) cc_final: 0.7237 (mmt) REVERT: J 44 ARG cc_start: 0.8681 (mmm-85) cc_final: 0.8423 (tmm-80) REVERT: J 63 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8681 (tm-30) REVERT: J 101 ARG cc_start: 0.8477 (mmm-85) cc_final: 0.8161 (tpp80) REVERT: J 207 MET cc_start: 0.6514 (OUTLIER) cc_final: 0.6294 (ttm) REVERT: K 76 MET cc_start: 0.7895 (mmt) cc_final: 0.7415 (tpp) REVERT: K 93 ASP cc_start: 0.7959 (t0) cc_final: 0.7746 (t0) REVERT: K 212 ARG cc_start: 0.7569 (ttt-90) cc_final: 0.6408 (ttm-80) REVERT: M 42 MET cc_start: 0.7958 (mmm) cc_final: 0.7311 (tpt) REVERT: M 50 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8110 (tp30) REVERT: M 79 ARG cc_start: 0.7864 (tpm170) cc_final: 0.7647 (tpm170) REVERT: M 96 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6192 (tt) REVERT: N 84 MET cc_start: 0.7258 (ttm) cc_final: 0.6957 (ttm) REVERT: N 88 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7307 (pp30) REVERT: a 28 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8135 (mm-30) REVERT: a 94 MET cc_start: 0.8239 (ttt) cc_final: 0.7986 (ttp) outliers start: 34 outliers final: 25 residues processed: 233 average time/residue: 0.1176 time to fit residues: 39.1011 Evaluate side-chains 239 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain a residue 96 ASP Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 130 PHE Chi-restraints excluded: chain a residue 138 PHE Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 268 LEU Chi-restraints excluded: chain a residue 315 THR Chi-restraints excluded: chain a residue 341 THR Chi-restraints excluded: chain a residue 348 VAL Chi-restraints excluded: chain a residue 351 ILE Chi-restraints excluded: chain a residue 352 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 90 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 15 optimal weight: 40.0000 chunk 72 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 27 optimal weight: 30.0000 chunk 83 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 113 GLN ** a 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.176563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.152943 restraints weight = 29577.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.152310 restraints weight = 18110.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.153241 restraints weight = 16287.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.153502 restraints weight = 11052.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.153897 restraints weight = 9983.911| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12423 Z= 0.116 Angle : 0.494 8.108 16900 Z= 0.263 Chirality : 0.034 0.167 2065 Planarity : 0.003 0.035 2306 Dihedral : 3.336 21.166 1973 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.32 % Favored : 97.63 % Rotamer: Outliers : 4.02 % Allowed : 32.44 % Favored : 63.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.97 (0.19), residues: 1856 helix: 3.47 (0.13), residues: 1442 sheet: 0.40 (0.62), residues: 77 loop : -0.98 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 104 TYR 0.015 0.001 TYR I 56 PHE 0.027 0.002 PHE a 335 TRP 0.007 0.001 TRP a 324 HIS 0.002 0.000 HIS a 216 Details of bonding type rmsd covalent geometry : bond 0.00248 (12423) covalent geometry : angle 0.49351 (16900) hydrogen bonds : bond 0.03234 ( 1225) hydrogen bonds : angle 3.29059 ( 3636) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 315 ASN cc_start: 0.7528 (m-40) cc_final: 0.7189 (t0) REVERT: G 317 GLN cc_start: 0.7897 (pm20) cc_final: 0.7440 (pm20) REVERT: I 26 LYS cc_start: 0.8195 (mmmt) cc_final: 0.7335 (tppt) REVERT: I 42 LYS cc_start: 0.8433 (ttpp) cc_final: 0.8039 (ttmm) REVERT: I 54 MET cc_start: 0.8469 (mmm) cc_final: 0.7673 (mmm) REVERT: I 62 LYS cc_start: 0.9275 (tppt) cc_final: 0.8949 (ttmt) REVERT: J 16 MET cc_start: 0.7425 (mmm) cc_final: 0.7138 (mmt) REVERT: J 44 ARG cc_start: 0.8690 (mmm-85) cc_final: 0.8454 (tmm-80) REVERT: J 63 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8663 (tm-30) REVERT: J 101 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.8066 (tpp80) REVERT: J 207 MET cc_start: 0.6675 (OUTLIER) cc_final: 0.6385 (ttm) REVERT: J 215 LEU cc_start: 0.8447 (tp) cc_final: 0.8124 (tp) REVERT: K 76 MET cc_start: 0.7886 (mmt) cc_final: 0.7408 (tpp) REVERT: K 212 ARG cc_start: 0.7524 (ttt-90) cc_final: 0.6277 (ttp-170) REVERT: M 42 MET cc_start: 0.7887 (mmm) cc_final: 0.7335 (tpt) REVERT: M 50 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8066 (tp30) REVERT: M 96 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6208 (tt) REVERT: N 84 MET cc_start: 0.7326 (ttm) cc_final: 0.6913 (ttm) REVERT: N 88 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7509 (pp30) REVERT: a 28 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8124 (mm-30) REVERT: a 94 MET cc_start: 0.8252 (ttt) cc_final: 0.8041 (ttp) REVERT: a 295 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8362 (tp) outliers start: 33 outliers final: 29 residues processed: 236 average time/residue: 0.1113 time to fit residues: 37.7973 Evaluate side-chains 239 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain a residue 96 ASP Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 130 PHE Chi-restraints excluded: chain a residue 138 PHE Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 256 GLU Chi-restraints excluded: chain a residue 261 VAL Chi-restraints excluded: chain a residue 268 LEU Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain a residue 315 THR Chi-restraints excluded: chain a residue 341 THR Chi-restraints excluded: chain a residue 348 VAL Chi-restraints excluded: chain a residue 351 ILE Chi-restraints excluded: chain a residue 352 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 125 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 175 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 15 optimal weight: 40.0000 chunk 146 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 53 GLN a 334 GLN ** a 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.173134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.149910 restraints weight = 29619.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.151549 restraints weight = 20510.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.151285 restraints weight = 14327.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.150822 restraints weight = 12246.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.151521 restraints weight = 9595.627| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12423 Z= 0.180 Angle : 0.587 13.892 16900 Z= 0.309 Chirality : 0.037 0.163 2065 Planarity : 0.003 0.043 2306 Dihedral : 3.576 21.228 1973 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.91 % Favored : 97.04 % Rotamer: Outliers : 4.63 % Allowed : 32.20 % Favored : 63.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.66 (0.19), residues: 1856 helix: 3.25 (0.13), residues: 1444 sheet: 0.06 (0.56), residues: 86 loop : -1.08 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 104 TYR 0.015 0.001 TYR I 56 PHE 0.029 0.002 PHE G 316 TRP 0.010 0.001 TRP a 188 HIS 0.002 0.001 HIS a 216 Details of bonding type rmsd covalent geometry : bond 0.00401 (12423) covalent geometry : angle 0.58652 (16900) hydrogen bonds : bond 0.03548 ( 1225) hydrogen bonds : angle 3.55677 ( 3636) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 315 ASN cc_start: 0.7729 (m-40) cc_final: 0.7525 (t0) REVERT: G 317 GLN cc_start: 0.8101 (pm20) cc_final: 0.7766 (pt0) REVERT: I 26 LYS cc_start: 0.8167 (mmmt) cc_final: 0.7439 (tppt) REVERT: I 42 LYS cc_start: 0.8500 (ttpp) cc_final: 0.8082 (ttmm) REVERT: I 62 LYS cc_start: 0.9277 (tppt) cc_final: 0.8944 (ttmt) REVERT: J 16 MET cc_start: 0.7365 (mmm) cc_final: 0.7147 (mmt) REVERT: J 44 ARG cc_start: 0.8708 (mmm-85) cc_final: 0.8448 (tmm-80) REVERT: J 63 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8686 (tm-30) REVERT: J 215 LEU cc_start: 0.8477 (tp) cc_final: 0.8060 (tp) REVERT: K 76 MET cc_start: 0.8083 (mmt) cc_final: 0.7626 (tpp) REVERT: K 212 ARG cc_start: 0.7688 (ttt-90) cc_final: 0.5526 (mtt180) REVERT: M 42 MET cc_start: 0.7998 (mmm) cc_final: 0.7379 (tpt) REVERT: M 50 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8052 (tp30) REVERT: M 96 LEU cc_start: 0.6290 (OUTLIER) cc_final: 0.5754 (tt) REVERT: N 84 MET cc_start: 0.7384 (ttm) cc_final: 0.6997 (ttm) REVERT: N 88 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7564 (pp30) REVERT: N 102 MET cc_start: 0.7358 (ttt) cc_final: 0.6994 (ttm) REVERT: a 28 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8127 (mm-30) REVERT: a 94 MET cc_start: 0.8305 (ttt) cc_final: 0.7736 (tmm) REVERT: a 295 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8387 (tp) REVERT: a 338 ARG cc_start: 0.8417 (tpp80) cc_final: 0.7931 (ttp-170) outliers start: 38 outliers final: 32 residues processed: 225 average time/residue: 0.1153 time to fit residues: 37.4759 Evaluate side-chains 231 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain a residue 111 ILE Chi-restraints excluded: chain a residue 113 THR Chi-restraints excluded: chain a residue 130 PHE Chi-restraints excluded: chain a residue 138 PHE Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 243 SER Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 256 GLU Chi-restraints excluded: chain a residue 261 VAL Chi-restraints excluded: chain a residue 268 LEU Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain a residue 315 THR Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 341 THR Chi-restraints excluded: chain a residue 348 VAL Chi-restraints excluded: chain a residue 352 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 34 optimal weight: 10.0000 chunk 180 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 165 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 137 optimal weight: 20.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 100 GLN ** a 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.176047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.152803 restraints weight = 29400.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.152280 restraints weight = 19280.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.152895 restraints weight = 17631.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.153190 restraints weight = 11723.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.153532 restraints weight = 10353.784| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12423 Z= 0.120 Angle : 0.528 11.530 16900 Z= 0.278 Chirality : 0.034 0.175 2065 Planarity : 0.003 0.050 2306 Dihedral : 3.411 23.580 1973 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.53 % Favored : 97.41 % Rotamer: Outliers : 4.39 % Allowed : 32.56 % Favored : 63.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.87 (0.19), residues: 1856 helix: 3.43 (0.13), residues: 1440 sheet: 0.09 (0.57), residues: 86 loop : -1.06 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 104 TYR 0.016 0.001 TYR I 56 PHE 0.019 0.002 PHE G 316 TRP 0.007 0.001 TRP G 107 HIS 0.001 0.000 HIS G 296 Details of bonding type rmsd covalent geometry : bond 0.00258 (12423) covalent geometry : angle 0.52843 (16900) hydrogen bonds : bond 0.03263 ( 1225) hydrogen bonds : angle 3.32080 ( 3636) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2365.64 seconds wall clock time: 41 minutes 16.43 seconds (2476.43 seconds total)