Starting phenix.real_space_refine on Sat Jun 29 10:51:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2i_18848/06_2024/8r2i_18848_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2i_18848/06_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_18848/06_2024/8r2i_18848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2i_18848/06_2024/8r2i_18848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2i_18848/06_2024/8r2i_18848_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2i_18848/06_2024/8r2i_18848_updated.pdb" } 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-5370/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: 13.22, per 1000 atoms: 0.73 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: 7.48 Conformation dependent library (CDL) restraints added in 2.5 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... running ksdssp... Secondary structure from input PDB file: 82 helices and 5 sheets defined 58.2% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 31 through 53 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 102 through 107 Processing helix chain 'A' and resid 110 through 136 Processing helix chain 'A' and resid 143 through 158 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 161 through 165 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 196 through 222 Processing helix chain 'A' and resid 248 through 258 Processing helix chain 'A' and resid 268 through 294 Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'B' and resid 8 through 12 removed outlier: 3.901A pdb=" N VAL B 12 " --> pdb=" O HIS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 44 Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 93 through 116 Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 135 through 156 Processing helix chain 'B' and resid 187 through 190 Processing helix chain 'B' and resid 195 through 218 removed outlier: 3.846A pdb=" N ALA B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 234 through 258 Processing helix chain 'B' and resid 265 through 268 No H-bonds generated for 'chain 'B' and resid 265 through 268' Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 307 through 312 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 392 through 395 No H-bonds generated for 'chain 'B' and resid 392 through 395' Processing helix chain 'B' and resid 414 through 424 Processing helix chain 'B' and resid 447 through 474 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 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'C' and resid 26 through 30 Processing helix chain 'C' and resid 34 through 61 Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 76 through 82 Processing helix chain 'C' and resid 97 through 122 Processing helix chain 'C' and resid 144 through 168 Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 194 through 202 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 218 through 241 Processing helix chain 'C' and resid 246 through 251 Processing helix chain 'C' and resid 256 through 280 Processing helix chain 'C' and resid 287 through 290 No H-bonds generated for 'chain 'C' and resid 287 through 290' Processing helix chain 'C' and resid 294 through 312 removed outlier: 3.909A pdb=" N SER C 298 " --> pdb=" O GLY C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 346 Processing helix chain 'C' and resid 355 through 357 No H-bonds generated for 'chain 'C' and resid 355 through 357' Processing helix chain 'C' and resid 365 through 368 No H-bonds generated for 'chain 'C' and resid 365 through 368' Processing helix chain 'C' and resid 374 through 385 Processing helix chain 'C' and resid 410 through 441 Processing helix chain 'D' and resid 14 through 23 Processing helix chain 'D' and resid 31 through 53 removed outlier: 4.245A pdb=" N LEU D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU D 36 " --> pdb=" O TRP D 32 " (cutoff:3.500A) Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 101 through 107 Processing helix chain 'D' and resid 109 through 136 Processing helix chain 'D' and resid 141 through 157 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 159 through 163 Processing helix chain 'D' and resid 167 through 169 No H-bonds generated for 'chain 'D' and resid 167 through 169' Processing helix chain 'D' and resid 175 through 189 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 195 through 217 Processing helix chain 'D' and resid 246 through 255 Processing helix chain 'D' and resid 264 through 290 Proline residue: D 275 - end of helix Processing helix chain 'D' and resid 299 through 307 Processing helix chain 'D' and resid 314 through 333 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 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'E' and resid 10 through 14 removed outlier: 3.669A pdb=" N LEU E 14 " --> pdb=" O PHE E 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 10 through 14' Processing helix chain 'E' and resid 17 through 39 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 42 through 47 Processing helix chain 'E' and resid 72 through 79 Processing helix chain 'F' and resid 17 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 25 through 34 Proline residue: H 32 - end of helix Processing helix chain 'H' and resid 47 through 68 Processing helix chain 'I' and resid 2 through 23 Processing helix chain 'K' and resid 13 through 43 Proline residue: K 17 - end of helix Proline residue: K 20 - end of helix removed outlier: 3.752A pdb=" N LEU K 25 " --> pdb=" O VAL K 22 " (cutoff:3.500A) Proline residue: K 26 - end of helix Proline residue: K 29 - end of helix removed outlier: 3.744A pdb=" N VAL K 43 " --> pdb=" O GLN K 40 " (cutoff:3.500A) Processing helix chain '2' and resid 33 through 49 Processing helix chain '2' and resid 55 through 75 Processing helix chain '2' and resid 79 through 82 No H-bonds generated for 'chain '2' and resid 79 through 82' Processing helix chain '2' and resid 85 through 102 Processing helix chain '2' and resid 112 through 129 Processing helix chain '1' and resid 3 through 23 removed outlier: 4.270A pdb=" N VAL 1 15 " --> pdb=" O SER 1 11 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL 1 16 " --> pdb=" O LEU 1 12 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER 1 17 " --> pdb=" O VAL 1 13 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ALA 1 18 " --> pdb=" O LEU 1 14 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLY 1 19 " --> pdb=" O VAL 1 15 " (cutoff:3.500A) Proline residue: 1 20 - end of helix Processing sheet with id= A, first strand: chain 'B' and resid 167 through 169 Processing sheet with id= B, first strand: chain 'B' and resid 343 through 347 Processing sheet with id= C, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.776A pdb=" N GLU B 431 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 369 through 371 Processing sheet with id= E, first strand: chain 'C' and resid 173 through 175 760 hydrogen bonds defined for protein. 2202 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: 5.03 Time building geometry restraints manager: 8.18 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: 1936 2.75 - 3.29: 17715 3.29 - 3.82: 32733 3.82 - 4.36: 38547 4.36 - 4.90: 65714 Nonbonded interactions: 156645 Sorted by model distance: nonbonded pdb=" O THR 2 47 " pdb=" NZ LYS 2 57 " model vdw 2.210 2.520 nonbonded pdb=" O TYR A 29 " pdb=" NH1 ARG A 129 " model vdw 2.251 2.520 nonbonded pdb=" OH TYR E 19 " pdb=" O SER 1 17 " model vdw 2.255 2.440 nonbonded pdb=" O TRP C 238 " pdb=" OG1 THR C 242 " model vdw 2.267 2.440 nonbonded pdb=" NH1 ARG B 124 " pdb=" O GLU H 19 " model vdw 2.270 2.520 ... (remaining 156640 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.980 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: 0.000 Extract box with map and model: 9.450 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 50.620 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 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:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.660 ------------------------------------------------------------------------------- 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= 1.154 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 : 1.442 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 1.2978 time to fit residues: 242.7925 Evaluate side-chains 114 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.761 ------------------------------------------------------------------------------- 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: 6.9990 chunk 141 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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: 0.8134 moved from start: 0.0821 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= 0.201 Angle : 0.917 44.188 26148 Z= 0.350 Chirality : 0.042 0.381 2517 Planarity : 0.004 0.056 3296 Dihedral : 21.003 166.004 3212 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.64 % Allowed : 7.72 % Favored : 91.63 % 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 (0.20), residues: 1897 helix: 2.08 (0.16), residues: 1118 sheet: -0.69 (0.82), residues: 42 loop : -0.06 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 131 HIS 0.004 0.001 HIS D 268 PHE 0.028 0.001 PHE B 246 TYR 0.009 0.001 TYR B 172 ARG 0.001 0.000 ARG F 44 *********************** 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 134 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 1.686 Fit side-chains revert: symmetry clash REVERT: E 17 ILE cc_start: 0.7832 (mm) cc_final: 0.7578 (tp) REVERT: E 77 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8542 (tmtt) REVERT: H 36 GLU cc_start: 0.7147 (tt0) cc_final: 0.6774 (tp30) outliers start: 10 outliers final: 4 residues processed: 126 average time/residue: 1.1615 time to fit residues: 166.9142 Evaluate side-chains 113 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain 1 residue 2 ASN Chi-restraints excluded: chain 1 residue 9 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 ASN 2 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 18838 Z= 0.432 Angle : 0.973 44.257 26148 Z= 0.388 Chirality : 0.046 0.304 2517 Planarity : 0.005 0.057 3296 Dihedral : 18.048 167.713 3212 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.61 % Allowed : 9.07 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.19), residues: 1897 helix: 1.77 (0.15), residues: 1125 sheet: -0.31 (0.94), residues: 35 loop : -0.20 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 131 HIS 0.006 0.002 HIS D 189 PHE 0.029 0.002 PHE B 246 TYR 0.019 0.002 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 135 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 1.684 Fit side-chains REVERT: E 17 ILE cc_start: 0.7986 (mm) cc_final: 0.7781 (tt) REVERT: E 77 LYS cc_start: 0.8812 (ttpt) cc_final: 0.8538 (tmtt) outliers start: 25 outliers final: 7 residues processed: 121 average time/residue: 1.3126 time to fit residues: 178.7220 Evaluate side-chains 110 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain 1 residue 2 ASN Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 14 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: 10.0000 chunk 127 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 2 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18838 Z= 0.179 Angle : 0.881 44.106 26148 Z= 0.340 Chirality : 0.040 0.242 2517 Planarity : 0.004 0.055 3296 Dihedral : 16.540 171.824 3212 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.03 % Allowed : 10.49 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.20), residues: 1897 helix: 1.97 (0.15), residues: 1137 sheet: -0.45 (0.89), residues: 37 loop : -0.10 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 131 HIS 0.005 0.001 HIS D 268 PHE 0.021 0.001 PHE B 246 TYR 0.008 0.001 TYR B 172 ARG 0.004 0.000 ARG E 18 *********************** 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 129 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 1.779 Fit side-chains REVERT: E 77 LYS cc_start: 0.8767 (ttpt) cc_final: 0.8523 (tmtt) REVERT: H 36 GLU cc_start: 0.7645 (tt0) cc_final: 0.7303 (tp30) outliers start: 16 outliers final: 8 residues processed: 122 average time/residue: 1.2133 time to fit residues: 168.3903 Evaluate side-chains 111 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 340 VAL 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 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: 1.9990 chunk 102 optimal weight: 7.9990 chunk 2 optimal weight: 0.0770 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN 2 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18838 Z= 0.216 Angle : 0.877 44.170 26148 Z= 0.339 Chirality : 0.041 0.248 2517 Planarity : 0.004 0.056 3296 Dihedral : 15.846 172.546 3212 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.35 % Allowed : 11.26 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.20), residues: 1897 helix: 2.02 (0.15), residues: 1130 sheet: -0.37 (0.90), residues: 37 loop : -0.10 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 131 HIS 0.004 0.001 HIS E 23 PHE 0.023 0.001 PHE B 246 TYR 0.009 0.001 TYR B 172 ARG 0.003 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 130 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 1.765 Fit side-chains revert: symmetry clash REVERT: E 77 LYS cc_start: 0.8769 (ttpt) cc_final: 0.8529 (tmtt) REVERT: H 36 GLU cc_start: 0.7680 (tt0) cc_final: 0.7233 (tp30) REVERT: H 76 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.7260 (t0) outliers start: 21 outliers final: 12 residues processed: 120 average time/residue: 1.2197 time to fit residues: 166.1512 Evaluate side-chains 117 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain D residue 14 TRP Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 340 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 76 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN 2 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1601 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= 0.225 Angle : 0.869 44.184 26148 Z= 0.337 Chirality : 0.041 0.258 2517 Planarity : 0.004 0.055 3296 Dihedral : 15.600 172.064 3212 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.74 % Allowed : 11.39 % Favored : 86.87 % 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: 1.75 (0.20), residues: 1897 helix: 2.03 (0.15), residues: 1131 sheet: -0.33 (0.90), residues: 37 loop : -0.10 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 131 HIS 0.004 0.001 HIS C 418 PHE 0.023 0.001 PHE B 246 TYR 0.010 0.001 TYR B 172 ARG 0.003 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 140 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 1.738 Fit side-chains REVERT: E 77 LYS cc_start: 0.8751 (ttpt) cc_final: 0.8523 (tmtt) REVERT: H 76 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7292 (t0) outliers start: 27 outliers final: 16 residues processed: 130 average time/residue: 1.1564 time to fit residues: 172.8377 Evaluate side-chains 123 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 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 10 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 14 TRP Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain 2 residue 59 ASP Chi-restraints excluded: chain 1 residue 2 ASN Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 16 VAL 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: 0.6980 chunk 103 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18838 Z= 0.244 Angle : 0.875 44.208 26148 Z= 0.342 Chirality : 0.041 0.253 2517 Planarity : 0.004 0.055 3296 Dihedral : 15.568 171.547 3212 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.35 % Allowed : 12.36 % Favored : 86.29 % 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: 2.01 (0.15), residues: 1131 sheet: -0.32 (0.90), residues: 37 loop : -0.10 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 131 HIS 0.004 0.001 HIS C 418 PHE 0.023 0.001 PHE B 246 TYR 0.010 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 132 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 1.792 Fit side-chains REVERT: E 77 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8514 (tmtt) REVERT: H 36 GLU cc_start: 0.7696 (tt0) cc_final: 0.7419 (tp30) REVERT: H 76 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7309 (t0) outliers start: 21 outliers final: 16 residues processed: 122 average time/residue: 1.2105 time to fit residues: 167.6030 Evaluate side-chains 123 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 14 TRP Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain 2 residue 82 SER Chi-restraints excluded: chain 1 residue 2 ASN Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 13 VAL 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: 3.9990 chunk 107 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 114 optimal weight: 5.9990 chunk 122 optimal weight: 0.0980 chunk 89 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 2 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18838 Z= 0.193 Angle : 0.857 44.158 26148 Z= 0.333 Chirality : 0.040 0.254 2517 Planarity : 0.004 0.054 3296 Dihedral : 15.373 172.654 3212 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.54 % Allowed : 12.42 % Favored : 86.04 % 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: 1.81 (0.20), residues: 1897 helix: 2.07 (0.15), residues: 1137 sheet: -0.38 (0.90), residues: 37 loop : -0.07 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 131 HIS 0.003 0.001 HIS D 268 PHE 0.021 0.001 PHE B 246 TYR 0.009 0.001 TYR B 172 ARG 0.002 0.000 ARG E 18 *********************** 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 135 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 111 time to evaluate : 1.782 Fit side-chains REVERT: D 352 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7712 (tp) REVERT: E 77 LYS cc_start: 0.8698 (ttpt) cc_final: 0.8480 (tmtt) REVERT: H 36 GLU cc_start: 0.7574 (tt0) cc_final: 0.7266 (tp30) REVERT: H 76 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7317 (t0) outliers start: 24 outliers final: 18 residues processed: 126 average time/residue: 1.1547 time to fit residues: 166.4124 Evaluate side-chains 127 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 14 TRP Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 287 VAL 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 F residue 20 LEU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain 2 residue 59 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 0.0020 chunk 172 optimal weight: 0.4980 chunk 157 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 151 optimal weight: 0.0050 chunk 158 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 overall best weight: 0.4602 ------------------------------------------------------------------------------- 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** H 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18838 Z= 0.144 Angle : 0.847 44.098 26148 Z= 0.329 Chirality : 0.039 0.234 2517 Planarity : 0.004 0.054 3296 Dihedral : 15.082 176.273 3212 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.29 % Allowed : 13.32 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.20), residues: 1897 helix: 2.19 (0.15), residues: 1131 sheet: -0.34 (0.90), residues: 37 loop : -0.05 (0.24), residues: 729 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 0.007 0.001 TYR B 314 ARG 0.003 0.000 ARG E 69 *********************** 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 133 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 1.678 Fit side-chains revert: symmetry clash REVERT: H 36 GLU cc_start: 0.7546 (tt0) cc_final: 0.7268 (tp30) REVERT: H 76 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7285 (t0) outliers start: 20 outliers final: 13 residues processed: 126 average time/residue: 1.0995 time to fit residues: 159.2892 Evaluate side-chains 121 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 14 TRP Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain 2 residue 59 ASP Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 13 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 148 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 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** ** 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: 0.8219 moved from start: 0.1879 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= 0.315 Angle : 0.900 44.307 26148 Z= 0.356 Chirality : 0.042 0.257 2517 Planarity : 0.004 0.056 3296 Dihedral : 15.353 170.607 3212 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.09 % Allowed : 13.77 % Favored : 85.14 % 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: 1.82 (0.20), residues: 1897 helix: 2.06 (0.15), residues: 1126 sheet: -0.34 (0.91), residues: 37 loop : 0.00 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 131 HIS 0.008 0.001 HIS A 195 PHE 0.025 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 124 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 1.867 Fit side-chains REVERT: E 24 SER cc_start: 0.8680 (t) cc_final: 0.7910 (p) REVERT: H 76 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7409 (t0) outliers start: 17 outliers final: 12 residues processed: 118 average time/residue: 1.0986 time to fit residues: 148.7607 Evaluate side-chains 118 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 14 TRP Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain 2 residue 59 ASP 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: 5.9990 chunk 45 optimal weight: 6.9990 chunk 136 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.076163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.056433 restraints weight = 45742.899| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.28 r_work: 0.2710 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18838 Z= 0.195 Angle : 0.869 44.121 26148 Z= 0.340 Chirality : 0.040 0.262 2517 Planarity : 0.004 0.054 3296 Dihedral : 15.214 171.539 3212 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.03 % Allowed : 13.71 % Favored : 85.26 % 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: 1.89 (0.20), residues: 1897 helix: 2.13 (0.15), residues: 1129 sheet: -0.38 (0.90), residues: 37 loop : -0.00 (0.24), residues: 731 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 0.031 0.001 PHE 2 101 TYR 0.009 0.001 TYR B 172 ARG 0.005 0.000 ARG B 384 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4442.70 seconds wall clock time: 79 minutes 34.22 seconds (4774.22 seconds total)