Starting phenix.real_space_refine on Wed Aug 7 18:00:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2i_18848/08_2024/8r2i_18848.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2i_18848/08_2024/8r2i_18848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2i_18848/08_2024/8r2i_18848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2i_18848/08_2024/8r2i_18848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2i_18848/08_2024/8r2i_18848.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2i_18848/08_2024/8r2i_18848.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 1 5.49 5 Mg 35 5.21 5 S 61 5.16 5 C 12425 2.51 5 N 2636 2.21 5 O 2894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 18054 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2390 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain breaks: 1 Chain: "B" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3811 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 25, 'TRANS': 461} Chain: "C" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3292 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 23, 'TRANS': 399} Chain: "D" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2674 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain breaks: 1 Chain: "E" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "F" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 269 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 2, 'TRANS': 30} Chain: "H" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 497 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "I" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 231 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "K" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 296 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 5, 'TRANS': 31} Chain: "2" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 790 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "1" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 224 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "A" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 294 Unusual residues: {'BCR': 1, 'BOG': 1, 'CLA': 3, 'FE2': 1, 'PHO': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 1195 Unusual residues: {'BCR': 2, 'CLA': 16, 'LHG': 1, 'LMG': 1, 'LMT': 2} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 977 Unusual residues: {'BCR': 3, 'BOG': 1, 'CLA': 13, 'DGD': 1} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 359 Unusual residues: {'BCR': 1, 'BCT': 1, 'BOG': 1, 'CLA': 3, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'BCR': 1, 'LMG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 10.61, per 1000 atoms: 0.59 Number of scatterers: 18054 At special positions: 0 Unit cell: (134.4, 107.52, 133.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 61 16.00 P 1 15.00 Mg 35 11.99 O 2894 8.00 N 2636 7.00 C 12425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=34, symmetry=0 Number of additional bonds: simple=34, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.64 Conformation dependent library (CDL) restraints added in 2.8 seconds 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3462 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 66.5% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 30 through 54 removed outlier: 3.699A pdb=" N ILE A 36 " --> pdb=" O TRP A 32 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 101 through 108 Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.840A pdb=" N GLN A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 159 removed outlier: 4.217A pdb=" N ALA A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 160 through 166 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 175 through 191 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 195 through 223 Processing helix chain 'A' and resid 248 through 259 Processing helix chain 'A' and resid 267 through 295 Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 316 through 333 Processing helix chain 'B' and resid 7 through 13 removed outlier: 3.901A pdb=" N VAL B 12 " --> pdb=" O HIS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 45 Processing helix chain 'B' and resid 62 through 69 Processing helix chain 'B' and resid 92 through 117 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 194 through 219 removed outlier: 4.009A pdb=" N ILE B 198 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 233 through 259 removed outlier: 3.882A pdb=" N VAL B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.788A pdb=" N TRP B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 294 removed outlier: 3.520A pdb=" N GLU B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 306 through 313 Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 413 through 425 Processing helix chain 'B' and resid 446 through 475 removed outlier: 3.599A pdb=" N PHE B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 479 Processing helix chain 'C' and resid 25 through 31 removed outlier: 3.567A pdb=" N ILE C 31 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 62 Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 75 through 83 removed outlier: 3.634A pdb=" N LEU C 83 " --> pdb=" O HIS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 122 removed outlier: 3.561A pdb=" N PHE C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 169 Processing helix chain 'C' and resid 178 through 182 removed outlier: 3.588A pdb=" N GLY C 181 " --> pdb=" O ALA C 178 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY C 182 " --> pdb=" O PRO C 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 178 through 182' Processing helix chain 'C' and resid 193 through 203 removed outlier: 4.120A pdb=" N TYR C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL C 202 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.819A pdb=" N SER C 214 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 215 " --> pdb=" O ILE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 242 removed outlier: 3.540A pdb=" N ILE C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 252 Processing helix chain 'C' and resid 255 through 281 Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 293 through 313 removed outlier: 3.909A pdb=" N SER C 298 " --> pdb=" O GLY C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 347 removed outlier: 3.731A pdb=" N THR C 343 " --> pdb=" O GLY C 340 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP C 347 " --> pdb=" O MET C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 356 No H-bonds generated for 'chain 'C' and resid 354 through 356' Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.706A pdb=" N LYS C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 409 through 442 Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 33 through 54 Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 100 through 108 Processing helix chain 'D' and resid 108 through 137 removed outlier: 4.106A pdb=" N ALA D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 removed outlier: 3.561A pdb=" N ILE D 144 " --> pdb=" O PRO D 140 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 158 through 164 Processing helix chain 'D' and resid 166 through 170 removed outlier: 3.526A pdb=" N PHE D 169 " --> pdb=" O GLY D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 190 Processing helix chain 'D' and resid 191 through 193 No H-bonds generated for 'chain 'D' and resid 191 through 193' Processing helix chain 'D' and resid 194 through 218 Processing helix chain 'D' and resid 245 through 256 Processing helix chain 'D' and resid 263 through 291 Proline residue: D 275 - end of helix Processing helix chain 'D' and resid 298 through 308 removed outlier: 3.662A pdb=" N GLU D 302 " --> pdb=" O PHE D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 334 removed outlier: 4.449A pdb=" N ALA D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN D 332 " --> pdb=" O TRP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 338 Processing helix chain 'E' and resid 9 through 15 removed outlier: 4.071A pdb=" N ILE E 13 " --> pdb=" O PRO E 9 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU E 14 " --> pdb=" O PHE E 10 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR E 15 " --> pdb=" O SER E 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 9 through 15' Processing helix chain 'E' and resid 18 through 40 removed outlier: 3.952A pdb=" N SER E 24 " --> pdb=" O TRP E 20 " (cutoff:3.500A) Proline residue: E 28 - end of helix Processing helix chain 'E' and resid 41 through 48 Processing helix chain 'E' and resid 71 through 80 removed outlier: 3.803A pdb=" N GLN E 75 " --> pdb=" O ASN E 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 41 Proline residue: F 28 - end of helix removed outlier: 3.985A pdb=" N PHE F 41 " --> pdb=" O THR F 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 35 Proline residue: H 32 - end of helix Processing helix chain 'H' and resid 46 through 69 Processing helix chain 'I' and resid 2 through 24 Processing helix chain 'K' and resid 12 through 17 Proline residue: K 17 - end of helix Processing helix chain 'K' and resid 18 through 25 Processing helix chain 'K' and resid 27 through 44 Processing helix chain '2' and resid 32 through 50 removed outlier: 3.732A pdb=" N GLU 2 36 " --> pdb=" O THR 2 32 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU 2 50 " --> pdb=" O VAL 2 46 " (cutoff:3.500A) Processing helix chain '2' and resid 54 through 76 removed outlier: 3.845A pdb=" N GLU 2 58 " --> pdb=" O ASP 2 54 " (cutoff:3.500A) Processing helix chain '2' and resid 78 through 83 Processing helix chain '2' and resid 84 through 103 removed outlier: 3.546A pdb=" N SER 2 103 " --> pdb=" O GLY 2 99 " (cutoff:3.500A) Processing helix chain '2' and resid 111 through 130 removed outlier: 3.892A pdb=" N THR 2 130 " --> pdb=" O THR 2 126 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 15 removed outlier: 3.539A pdb=" N ALA 1 6 " --> pdb=" O ASN 1 2 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL 1 15 " --> pdb=" O SER 1 11 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 24 removed outlier: 3.710A pdb=" N VAL 1 22 " --> pdb=" O ALA 1 18 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 167 through 169 Processing sheet with id=AA2, first strand: chain 'B' and resid 322 through 323 removed outlier: 7.509A pdb=" N GLY B 322 " --> pdb=" O ARG D 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 336 through 340 removed outlier: 5.725A pdb=" N ALA B 337 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASP B 433 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY B 339 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 377 through 380 removed outlier: 3.703A pdb=" N PHE B 346 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 356 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N ALA B 344 " --> pdb=" O VAL B 356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AA6, first strand: chain 'C' and resid 330 through 331 Processing sheet with id=AA7, first strand: chain 'C' and resid 358 through 359 removed outlier: 3.799A pdb=" N GLY C 362 " --> pdb=" O GLY C 359 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 77 through 78 897 hydrogen bonds defined for protein. 2577 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: 5.01 Time building geometry restraints manager: 8.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.41: 7863 1.41 - 1.61: 10694 1.61 - 1.81: 137 1.81 - 2.01: 35 2.01 - 2.21: 109 Bond restraints: 18838 Sorted by residual: bond pdb=" C25 BCR B 517 " pdb=" C26 BCR B 517 " ideal model delta sigma weight residual 1.347 1.611 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C25 BCR H 101 " pdb=" C26 BCR H 101 " ideal model delta sigma weight residual 1.347 1.608 -0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C25 BCR C 515 " pdb=" C26 BCR C 515 " ideal model delta sigma weight residual 1.347 1.607 -0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" C25 BCR C 516 " pdb=" C26 BCR C 516 " ideal model delta sigma weight residual 1.347 1.606 -0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C25 BCR A 406 " pdb=" C26 BCR A 406 " ideal model delta sigma weight residual 1.347 1.606 -0.259 2.00e-02 2.50e+03 1.68e+02 ... (remaining 18833 not shown) Histogram of bond angle deviations from ideal: 77.09 - 97.06: 148 97.06 - 117.03: 12736 117.03 - 137.00: 13116 137.00 - 156.97: 74 156.97 - 176.94: 74 Bond angle restraints: 26148 Sorted by residual: angle pdb=" CBD CLA C 513 " pdb=" CGD CLA C 513 " pdb=" O1D CLA C 513 " ideal model delta sigma weight residual 127.77 80.37 47.40 3.00e+00 1.11e-01 2.50e+02 angle pdb=" CBD CLA C 513 " pdb=" CGD CLA C 513 " pdb=" O2D CLA C 513 " ideal model delta sigma weight residual 113.93 159.37 -45.44 3.00e+00 1.11e-01 2.29e+02 angle pdb=" C2 CLA B 502 " pdb=" C3 CLA B 502 " pdb=" C4 CLA B 502 " ideal model delta sigma weight residual 122.00 81.82 40.18 3.00e+00 1.11e-01 1.79e+02 angle pdb=" C4 CLA B 502 " pdb=" C3 CLA B 502 " pdb=" C5 CLA B 502 " ideal model delta sigma weight residual 117.04 77.09 39.95 3.00e+00 1.11e-01 1.77e+02 angle pdb=" O1D CLA C 513 " pdb=" CGD CLA C 513 " pdb=" O2D CLA C 513 " ideal model delta sigma weight residual 118.28 79.12 39.16 3.00e+00 1.11e-01 1.70e+02 ... (remaining 26143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.55: 9341 32.55 - 65.11: 445 65.11 - 97.66: 49 97.66 - 130.22: 78 130.22 - 162.77: 1 Dihedral angle restraints: 9914 sinusoidal: 4482 harmonic: 5432 Sorted by residual: dihedral pdb=" C3A DGD C 517 " pdb=" C1A DGD C 517 " pdb=" C2A DGD C 517 " pdb=" O1A DGD C 517 " ideal model delta sinusoidal sigma weight residual 335.78 173.01 162.77 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C4D PHO D 402 " pdb=" CBD PHO D 402 " pdb=" CHA PHO D 402 " pdb=" CGD PHO D 402 " ideal model delta sinusoidal sigma weight residual 243.52 115.98 127.54 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" CA THR D 217 " pdb=" C THR D 217 " pdb=" N VAL D 218 " pdb=" CA VAL D 218 " ideal model delta harmonic sigma weight residual 180.00 159.42 20.58 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 9911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 2475 0.154 - 0.308: 7 0.308 - 0.461: 0 0.461 - 0.615: 11 0.615 - 0.769: 24 Chirality restraints: 2517 Sorted by residual: chirality pdb=" C3A CLA B 504 " pdb=" C2A CLA B 504 " pdb=" C4A CLA B 504 " pdb=" CMA CLA B 504 " both_signs ideal model delta sigma weight residual False -2.76 -2.00 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" C3A CLA C 504 " pdb=" C2A CLA C 504 " pdb=" C4A CLA C 504 " pdb=" CMA CLA C 504 " both_signs ideal model delta sigma weight residual False -2.76 -2.02 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" C3A CLA C 511 " pdb=" C2A CLA C 511 " pdb=" C4A CLA C 511 " pdb=" CMA CLA C 511 " both_signs ideal model delta sigma weight residual False -2.76 -2.04 -0.72 2.00e-01 2.50e+01 1.30e+01 ... (remaining 2514 not shown) Planarity restraints: 3296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PHO A 404 " -0.094 2.00e-02 2.50e+03 1.12e-01 1.01e+03 pdb=" ND PHO A 404 " -0.055 2.00e-02 2.50e+03 pdb=" C1A PHO A 404 " -0.014 2.00e-02 2.50e+03 pdb=" C1B PHO A 404 " -0.044 2.00e-02 2.50e+03 pdb=" C1C PHO A 404 " -0.020 2.00e-02 2.50e+03 pdb=" C1D PHO A 404 " 0.009 2.00e-02 2.50e+03 pdb=" C2A PHO A 404 " 0.097 2.00e-02 2.50e+03 pdb=" C2B PHO A 404 " 0.113 2.00e-02 2.50e+03 pdb=" C2C PHO A 404 " -0.063 2.00e-02 2.50e+03 pdb=" C2D PHO A 404 " 0.053 2.00e-02 2.50e+03 pdb=" C3A PHO A 404 " -0.288 2.00e-02 2.50e+03 pdb=" C3B PHO A 404 " 0.142 2.00e-02 2.50e+03 pdb=" C3C PHO A 404 " -0.060 2.00e-02 2.50e+03 pdb=" C3D PHO A 404 " 0.056 2.00e-02 2.50e+03 pdb=" C4A PHO A 404 " -0.193 2.00e-02 2.50e+03 pdb=" C4B PHO A 404 " 0.006 2.00e-02 2.50e+03 pdb=" C4C PHO A 404 " -0.007 2.00e-02 2.50e+03 pdb=" C4D PHO A 404 " 0.005 2.00e-02 2.50e+03 pdb=" CAB PHO A 404 " 0.263 2.00e-02 2.50e+03 pdb=" CAC PHO A 404 " -0.096 2.00e-02 2.50e+03 pdb=" CAD PHO A 404 " 0.081 2.00e-02 2.50e+03 pdb=" CBD PHO A 404 " 0.104 2.00e-02 2.50e+03 pdb=" CHA PHO A 404 " 0.028 2.00e-02 2.50e+03 pdb=" CHB PHO A 404 " -0.125 2.00e-02 2.50e+03 pdb=" CHC PHO A 404 " -0.022 2.00e-02 2.50e+03 pdb=" CHD PHO A 404 " 0.028 2.00e-02 2.50e+03 pdb=" CMB PHO A 404 " 0.192 2.00e-02 2.50e+03 pdb=" CMC PHO A 404 " -0.110 2.00e-02 2.50e+03 pdb=" CMD PHO A 404 " 0.095 2.00e-02 2.50e+03 pdb=" NA PHO A 404 " -0.183 2.00e-02 2.50e+03 pdb=" NC PHO A 404 " 0.017 2.00e-02 2.50e+03 pdb=" OBD PHO A 404 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO D 402 " 0.037 2.00e-02 2.50e+03 5.50e-02 2.42e+02 pdb=" ND PHO D 402 " 0.126 2.00e-02 2.50e+03 pdb=" C1A PHO D 402 " 0.012 2.00e-02 2.50e+03 pdb=" C1B PHO D 402 " 0.007 2.00e-02 2.50e+03 pdb=" C1C PHO D 402 " 0.018 2.00e-02 2.50e+03 pdb=" C1D PHO D 402 " 0.020 2.00e-02 2.50e+03 pdb=" C2A PHO D 402 " 0.147 2.00e-02 2.50e+03 pdb=" C2B PHO D 402 " 0.007 2.00e-02 2.50e+03 pdb=" C2C PHO D 402 " 0.004 2.00e-02 2.50e+03 pdb=" C2D PHO D 402 " -0.004 2.00e-02 2.50e+03 pdb=" C3A PHO D 402 " -0.106 2.00e-02 2.50e+03 pdb=" C3B PHO D 402 " 0.024 2.00e-02 2.50e+03 pdb=" C3C PHO D 402 " -0.029 2.00e-02 2.50e+03 pdb=" C3D PHO D 402 " 0.015 2.00e-02 2.50e+03 pdb=" C4A PHO D 402 " -0.076 2.00e-02 2.50e+03 pdb=" C4B PHO D 402 " 0.038 2.00e-02 2.50e+03 pdb=" C4C PHO D 402 " -0.029 2.00e-02 2.50e+03 pdb=" C4D PHO D 402 " 0.050 2.00e-02 2.50e+03 pdb=" CAB PHO D 402 " 0.014 2.00e-02 2.50e+03 pdb=" CAC PHO D 402 " -0.058 2.00e-02 2.50e+03 pdb=" CAD PHO D 402 " 0.010 2.00e-02 2.50e+03 pdb=" CBD PHO D 402 " -0.079 2.00e-02 2.50e+03 pdb=" CHA PHO D 402 " -0.004 2.00e-02 2.50e+03 pdb=" CHB PHO D 402 " -0.020 2.00e-02 2.50e+03 pdb=" CHC PHO D 402 " 0.040 2.00e-02 2.50e+03 pdb=" CHD PHO D 402 " -0.052 2.00e-02 2.50e+03 pdb=" CMB PHO D 402 " -0.028 2.00e-02 2.50e+03 pdb=" CMC PHO D 402 " 0.014 2.00e-02 2.50e+03 pdb=" CMD PHO D 402 " -0.043 2.00e-02 2.50e+03 pdb=" NA PHO D 402 " -0.113 2.00e-02 2.50e+03 pdb=" NC PHO D 402 " 0.001 2.00e-02 2.50e+03 pdb=" OBD PHO D 402 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3D CLA A 402 " -0.044 2.00e-02 2.50e+03 8.52e-02 7.26e+01 pdb=" CAD CLA A 402 " 0.147 2.00e-02 2.50e+03 pdb=" CBD CLA A 402 " -0.042 2.00e-02 2.50e+03 pdb=" OBD CLA A 402 " -0.061 2.00e-02 2.50e+03 ... (remaining 3293 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1924 2.75 - 3.29: 17605 3.29 - 3.82: 32570 3.82 - 4.36: 38321 4.36 - 4.90: 65677 Nonbonded interactions: 156097 Sorted by model distance: nonbonded pdb=" O THR 2 47 " pdb=" NZ LYS 2 57 " model vdw 2.210 3.120 nonbonded pdb=" O TYR A 29 " pdb=" NH1 ARG A 129 " model vdw 2.251 3.120 nonbonded pdb=" OH TYR E 19 " pdb=" O SER 1 17 " model vdw 2.255 3.040 nonbonded pdb=" O TRP C 238 " pdb=" OG1 THR C 242 " model vdw 2.267 3.040 nonbonded pdb=" NH1 ARG B 124 " pdb=" O GLU H 19 " model vdw 2.270 3.120 ... (remaining 156092 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 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: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 47.290 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.021 0.264 18838 Z= 1.146 Angle : 1.619 47.403 26148 Z= 0.573 Chirality : 0.088 0.769 2517 Planarity : 0.008 0.112 3296 Dihedral : 21.202 162.774 6452 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.20), residues: 1897 helix: 1.83 (0.15), residues: 1142 sheet: 0.33 (0.96), residues: 32 loop : -0.12 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 131 HIS 0.007 0.001 HIS B 466 PHE 0.039 0.001 PHE D 185 TYR 0.016 0.001 TYR H 68 ARG 0.004 0.000 ARG E 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.726 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 1.2917 time to fit residues: 241.8178 Evaluate side-chains 114 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 189 HIS ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18838 Z= 0.271 Angle : 0.942 44.406 26148 Z= 0.370 Chirality : 0.044 0.335 2517 Planarity : 0.005 0.057 3296 Dihedral : 21.101 166.377 3212 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.77 % Allowed : 7.98 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.20), residues: 1897 helix: 1.93 (0.15), residues: 1135 sheet: -0.53 (0.90), residues: 37 loop : -0.07 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 131 HIS 0.004 0.001 HIS C 418 PHE 0.028 0.001 PHE B 246 TYR 0.010 0.001 TYR E 44 ARG 0.003 0.000 ARG C 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 1.745 Fit side-chains REVERT: E 24 SER cc_start: 0.8596 (m) cc_final: 0.8065 (p) REVERT: E 77 LYS cc_start: 0.8829 (ttpt) cc_final: 0.8553 (tmtt) REVERT: H 36 GLU cc_start: 0.7224 (tt0) cc_final: 0.6880 (tp30) outliers start: 12 outliers final: 6 residues processed: 123 average time/residue: 1.1880 time to fit residues: 166.6149 Evaluate side-chains 116 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain 1 residue 2 ASN Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 16 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 170 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 HIS ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 18838 Z= 0.364 Angle : 0.952 44.648 26148 Z= 0.379 Chirality : 0.045 0.312 2517 Planarity : 0.005 0.058 3296 Dihedral : 18.045 168.633 3212 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.09 % Allowed : 9.27 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.19), residues: 1897 helix: 1.84 (0.15), residues: 1129 sheet: -0.37 (0.95), residues: 35 loop : -0.10 (0.24), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 131 HIS 0.005 0.001 HIS D 189 PHE 0.027 0.002 PHE B 246 TYR 0.014 0.001 TYR H 68 ARG 0.003 0.000 ARG B 472 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 1.699 Fit side-chains REVERT: E 77 LYS cc_start: 0.8798 (ttpt) cc_final: 0.8523 (tmtt) REVERT: H 36 GLU cc_start: 0.7638 (tt0) cc_final: 0.7127 (tp30) outliers start: 17 outliers final: 7 residues processed: 125 average time/residue: 1.1832 time to fit residues: 168.3830 Evaluate side-chains 111 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain 1 residue 2 ASN Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 16 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 89 optimal weight: 0.0370 chunk 161 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 overall best weight: 1.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18838 Z= 0.223 Angle : 0.895 44.424 26148 Z= 0.351 Chirality : 0.042 0.328 2517 Planarity : 0.004 0.057 3296 Dihedral : 16.680 170.753 3212 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.09 % Allowed : 11.13 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.19), residues: 1897 helix: 1.92 (0.15), residues: 1136 sheet: -0.38 (0.95), residues: 35 loop : -0.09 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 131 HIS 0.004 0.001 HIS D 189 PHE 0.023 0.001 PHE B 246 TYR 0.010 0.001 TYR H 68 ARG 0.003 0.000 ARG C 345 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.718 Fit side-chains REVERT: E 24 SER cc_start: 0.8736 (t) cc_final: 0.7986 (p) REVERT: E 77 LYS cc_start: 0.8765 (ttpt) cc_final: 0.8548 (tmtt) REVERT: H 36 GLU cc_start: 0.7611 (tt0) cc_final: 0.7204 (tp30) outliers start: 17 outliers final: 8 residues processed: 124 average time/residue: 1.2248 time to fit residues: 174.0546 Evaluate side-chains 114 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain 1 residue 2 ASN Chi-restraints excluded: chain 1 residue 9 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 154 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18838 Z= 0.165 Angle : 0.866 44.295 26148 Z= 0.339 Chirality : 0.041 0.333 2517 Planarity : 0.004 0.056 3296 Dihedral : 15.684 174.051 3212 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.35 % Allowed : 11.71 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.20), residues: 1897 helix: 1.98 (0.15), residues: 1152 sheet: -0.56 (0.89), residues: 37 loop : -0.09 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 131 HIS 0.003 0.001 HIS C 225 PHE 0.020 0.001 PHE B 246 TYR 0.009 0.001 TYR D 244 ARG 0.002 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 1.941 Fit side-chains revert: symmetry clash REVERT: B 60 MET cc_start: 0.9216 (mmp) cc_final: 0.8716 (mmp) REVERT: E 24 SER cc_start: 0.8616 (t) cc_final: 0.7865 (p) outliers start: 21 outliers final: 11 residues processed: 129 average time/residue: 1.2446 time to fit residues: 182.8068 Evaluate side-chains 115 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain 2 residue 50 LEU Chi-restraints excluded: chain 1 residue 2 ASN Chi-restraints excluded: chain 1 residue 9 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 180 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18838 Z= 0.248 Angle : 0.884 44.446 26148 Z= 0.349 Chirality : 0.042 0.366 2517 Planarity : 0.004 0.057 3296 Dihedral : 15.556 172.604 3212 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.61 % Allowed : 12.61 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.19), residues: 1897 helix: 1.98 (0.15), residues: 1137 sheet: -0.35 (0.93), residues: 35 loop : -0.07 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 131 HIS 0.004 0.001 HIS D 189 PHE 0.024 0.001 PHE B 246 TYR 0.010 0.001 TYR B 172 ARG 0.004 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 1.648 Fit side-chains revert: symmetry clash REVERT: E 24 SER cc_start: 0.8660 (t) cc_final: 0.7872 (p) REVERT: H 36 GLU cc_start: 0.7578 (tt0) cc_final: 0.7353 (tp30) outliers start: 25 outliers final: 14 residues processed: 126 average time/residue: 1.2194 time to fit residues: 174.5467 Evaluate side-chains 120 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain 1 residue 2 ASN Chi-restraints excluded: chain 1 residue 9 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 152 optimal weight: 0.4980 chunk 101 optimal weight: 5.9990 chunk 180 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18838 Z= 0.169 Angle : 0.869 44.339 26148 Z= 0.342 Chirality : 0.041 0.389 2517 Planarity : 0.004 0.055 3296 Dihedral : 15.388 173.575 3212 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.42 % Allowed : 13.51 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.19), residues: 1897 helix: 2.04 (0.15), residues: 1138 sheet: -0.56 (0.88), residues: 37 loop : -0.05 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 131 HIS 0.003 0.001 HIS C 418 PHE 0.022 0.001 PHE B 246 TYR 0.008 0.001 TYR B 172 ARG 0.003 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 1.875 Fit side-chains revert: symmetry clash REVERT: D 352 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7681 (tp) REVERT: E 24 SER cc_start: 0.8649 (t) cc_final: 0.7874 (p) REVERT: H 36 GLU cc_start: 0.7447 (tt0) cc_final: 0.7195 (tp30) outliers start: 22 outliers final: 12 residues processed: 128 average time/residue: 1.2093 time to fit residues: 176.1113 Evaluate side-chains 121 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain 1 residue 2 ASN Chi-restraints excluded: chain 1 residue 9 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 0.0980 chunk 114 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18838 Z= 0.255 Angle : 0.895 44.509 26148 Z= 0.356 Chirality : 0.042 0.363 2517 Planarity : 0.004 0.057 3296 Dihedral : 15.469 172.301 3212 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.67 % Allowed : 13.71 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.19), residues: 1897 helix: 1.96 (0.15), residues: 1140 sheet: -0.31 (0.93), residues: 35 loop : -0.06 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 131 HIS 0.004 0.001 HIS D 189 PHE 0.023 0.001 PHE B 246 TYR 0.010 0.001 TYR E 19 ARG 0.002 0.000 ARG B 472 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 1.733 Fit side-chains revert: symmetry clash REVERT: D 352 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7709 (tp) REVERT: E 24 SER cc_start: 0.8637 (t) cc_final: 0.7835 (p) REVERT: H 36 GLU cc_start: 0.7622 (tt0) cc_final: 0.7346 (tp30) REVERT: 2 129 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7281 (mp) outliers start: 26 outliers final: 13 residues processed: 131 average time/residue: 1.2322 time to fit residues: 183.4303 Evaluate side-chains 123 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain 2 residue 129 LEU Chi-restraints excluded: chain 1 residue 2 ASN Chi-restraints excluded: chain 1 residue 9 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 157 optimal weight: 0.6980 chunk 167 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 158 optimal weight: 0.1980 chunk 110 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18838 Z= 0.235 Angle : 0.897 44.464 26148 Z= 0.357 Chirality : 0.042 0.362 2517 Planarity : 0.004 0.055 3296 Dihedral : 15.413 171.498 3212 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.22 % Allowed : 14.22 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.19), residues: 1897 helix: 1.97 (0.15), residues: 1139 sheet: -0.35 (0.92), residues: 35 loop : -0.07 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 131 HIS 0.004 0.001 HIS D 189 PHE 0.022 0.001 PHE B 246 TYR 0.010 0.001 TYR B 172 ARG 0.002 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 1.842 Fit side-chains revert: symmetry clash REVERT: D 352 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7697 (tp) REVERT: E 24 SER cc_start: 0.8617 (t) cc_final: 0.7836 (p) REVERT: H 36 GLU cc_start: 0.7609 (tt0) cc_final: 0.7326 (tp30) REVERT: 2 129 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7257 (mp) outliers start: 19 outliers final: 13 residues processed: 125 average time/residue: 1.2172 time to fit residues: 172.6899 Evaluate side-chains 123 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain 2 residue 129 LEU Chi-restraints excluded: chain 1 residue 2 ASN Chi-restraints excluded: chain 1 residue 9 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18838 Z= 0.322 Angle : 0.927 44.673 26148 Z= 0.374 Chirality : 0.044 0.335 2517 Planarity : 0.005 0.057 3296 Dihedral : 15.572 169.291 3212 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.09 % Allowed : 14.61 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.19), residues: 1897 helix: 1.90 (0.15), residues: 1132 sheet: -0.36 (0.93), residues: 35 loop : -0.10 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 247 HIS 0.006 0.001 HIS D 189 PHE 0.023 0.001 PHE B 246 TYR 0.012 0.001 TYR B 172 ARG 0.003 0.000 ARG E 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 1.732 Fit side-chains revert: symmetry clash REVERT: D 352 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7762 (tp) REVERT: E 24 SER cc_start: 0.8653 (t) cc_final: 0.7832 (p) outliers start: 17 outliers final: 14 residues processed: 119 average time/residue: 1.3151 time to fit residues: 177.2624 Evaluate side-chains 121 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain 1 residue 2 ASN Chi-restraints excluded: chain 1 residue 9 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.0060 chunk 130 optimal weight: 3.9990 overall best weight: 1.2158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.076420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.056654 restraints weight = 45751.990| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.28 r_work: 0.2716 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18838 Z= 0.196 Angle : 0.893 44.412 26148 Z= 0.355 Chirality : 0.042 0.344 2517 Planarity : 0.004 0.055 3296 Dihedral : 15.395 171.165 3212 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.03 % Allowed : 14.61 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.19), residues: 1897 helix: 2.00 (0.15), residues: 1133 sheet: -0.42 (0.93), residues: 35 loop : -0.10 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 131 HIS 0.004 0.001 HIS C 418 PHE 0.023 0.001 PHE B 246 TYR 0.009 0.001 TYR B 172 ARG 0.002 0.000 ARG E 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4433.06 seconds wall clock time: 79 minutes 20.43 seconds (4760.43 seconds total)