Starting phenix.real_space_refine on Sat May 11 06:27:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2i_18848/05_2024/8r2i_18848_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2i_18848/05_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_18848/05_2024/8r2i_18848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2i_18848/05_2024/8r2i_18848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2i_18848/05_2024/8r2i_18848_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2i_18848/05_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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: 10.57, 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: 8.77 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... 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: 3.14 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: 4.52 Time building geometry restraints manager: 9.32 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: 0.010 Normalize map: mean=0, sd=1: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 9.210 Check model and map are aligned: 0.120 Set scattering table: 0.180 Process input model: 50.990 Find NCS groups from input model: 0.470 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:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.890 ------------------------------------------------------------------------------- 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 : 1.704 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 1.3599 time to fit residues: 254.8012 Evaluate side-chains 114 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.895 ------------------------------------------------------------------------------- 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: 1.9990 chunk 146 optimal weight: 0.8980 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: 1.3786 ------------------------------------------------------------------------------- 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: 0.8127 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18838 Z= 0.201 Angle : 0.918 44.332 26148 Z= 0.352 Chirality : 0.042 0.403 2517 Planarity : 0.004 0.056 3296 Dihedral : 20.936 165.983 3212 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.58 % Allowed : 7.66 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.20), residues: 1897 helix: 1.95 (0.16), residues: 1122 sheet: -0.69 (0.82), residues: 42 loop : -0.09 (0.24), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 131 HIS 0.006 0.001 HIS B 466 PHE 0.027 0.001 PHE B 246 TYR 0.009 0.001 TYR B 172 ARG 0.002 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 133 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 1.697 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: 0.8538 (tmtt) REVERT: H 36 GLU cc_start: 0.7147 (tt0) cc_final: 0.6757 (tp30) outliers start: 9 outliers final: 4 residues processed: 126 average time/residue: 1.2494 time to fit residues: 179.5196 Evaluate side-chains 113 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 1.899 ------------------------------------------------------------------------------- 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: 1.9990 chunk 141 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 151 optimal weight: 8.9990 chunk 168 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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: 0.8256 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 18838 Z= 0.474 Angle : 0.997 44.416 26148 Z= 0.401 Chirality : 0.047 0.328 2517 Planarity : 0.005 0.058 3296 Dihedral : 18.212 167.473 3212 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.61 % Allowed : 9.27 % Favored : 89.12 % 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: 1.24 (0.19), residues: 1897 helix: 1.57 (0.15), residues: 1125 sheet: -0.32 (0.95), residues: 35 loop : -0.21 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 115 HIS 0.011 0.002 HIS B 114 PHE 0.030 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 : 1.898 Fit side-chains REVERT: E 17 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7793 (OUTLIER) REVERT: E 77 LYS cc_start: 0.8844 (ttpt) cc_final: 0.8561 (tmtt) outliers start: 25 outliers final: 8 residues processed: 120 average time/residue: 1.4061 time to fit residues: 189.7924 Evaluate side-chains 112 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 484 ASP 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 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: 8.9990 chunk 127 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 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** C 315 ASN ** 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: 0.8176 moved from start: 0.1443 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= 0.191 Angle : 0.889 44.112 26148 Z= 0.345 Chirality : 0.040 0.241 2517 Planarity : 0.004 0.057 3296 Dihedral : 16.630 171.869 3212 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.09 % Allowed : 11.00 % Favored : 87.90 % 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: 1.49 (0.20), residues: 1897 helix: 1.75 (0.15), residues: 1140 sheet: -0.46 (0.90), residues: 37 loop : -0.09 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 131 HIS 0.005 0.001 HIS B 114 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 131 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.855 Fit side-chains REVERT: E 77 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8500 (tmtt) REVERT: H 36 GLU cc_start: 0.7702 (tt0) cc_final: 0.7306 (tp30) outliers start: 17 outliers final: 9 residues processed: 125 average time/residue: 1.2742 time to fit residues: 180.8124 Evaluate side-chains 113 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 1.874 ------------------------------------------------------------------------------- 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 E residue 24 SER 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: 5.9990 chunk 2 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN 2 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18838 Z= 0.269 Angle : 0.895 44.180 26148 Z= 0.350 Chirality : 0.042 0.266 2517 Planarity : 0.005 0.056 3296 Dihedral : 16.091 171.719 3212 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.54 % Allowed : 11.71 % Favored : 86.74 % 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: 1.50 (0.20), residues: 1897 helix: 1.77 (0.15), residues: 1133 sheet: -0.42 (0.90), residues: 37 loop : -0.10 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 131 HIS 0.005 0.001 HIS C 106 PHE 0.025 0.001 PHE B 246 TYR 0.011 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 132 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 1.856 Fit side-chains revert: symmetry clash REVERT: E 77 LYS cc_start: 0.8767 (ttpt) cc_final: 0.8520 (tmtt) REVERT: H 76 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7298 (t0) outliers start: 24 outliers final: 12 residues processed: 123 average time/residue: 1.2652 time to fit residues: 176.7962 Evaluate side-chains 115 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 1.839 ------------------------------------------------------------------------------- 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 14 TRP 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 0.5980 chunk 162 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.8169 moved from start: 0.1543 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= 0.185 Angle : 0.866 44.138 26148 Z= 0.336 Chirality : 0.040 0.257 2517 Planarity : 0.004 0.055 3296 Dihedral : 15.639 173.180 3212 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.74 % Allowed : 11.90 % Favored : 86.36 % 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: 1.61 (0.20), residues: 1897 helix: 1.85 (0.15), residues: 1139 sheet: -0.36 (0.90), residues: 37 loop : -0.05 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 131 HIS 0.005 0.001 HIS C 106 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 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 143 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 116 time to evaluate : 1.918 Fit side-chains REVERT: E 77 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8454 (tmtt) REVERT: H 36 GLU cc_start: 0.7656 (tt0) cc_final: 0.7397 (tp30) outliers start: 27 outliers final: 17 residues processed: 135 average time/residue: 1.2590 time to fit residues: 193.8557 Evaluate side-chains 123 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 1.832 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 103 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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: 0.8165 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18838 Z= 0.186 Angle : 0.867 44.122 26148 Z= 0.338 Chirality : 0.040 0.257 2517 Planarity : 0.004 0.054 3296 Dihedral : 15.438 173.981 3212 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.61 % Allowed : 12.68 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.20), residues: 1897 helix: 1.92 (0.15), residues: 1127 sheet: -0.35 (0.90), residues: 37 loop : -0.04 (0.24), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 131 HIS 0.005 0.001 HIS C 106 PHE 0.022 0.001 PHE B 246 TYR 0.009 0.001 TYR B 172 ARG 0.002 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 139 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 1.716 Fit side-chains revert: symmetry clash REVERT: D 352 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7721 (tp) REVERT: E 77 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8480 (tmtt) REVERT: H 36 GLU cc_start: 0.7625 (tt0) cc_final: 0.7234 (tp30) REVERT: H 76 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7294 (t0) outliers start: 25 outliers final: 17 residues processed: 130 average time/residue: 1.2248 time to fit residues: 181.7512 Evaluate side-chains 126 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 1.856 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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: 0.8142 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18838 Z= 0.161 Angle : 0.856 44.104 26148 Z= 0.332 Chirality : 0.039 0.248 2517 Planarity : 0.004 0.054 3296 Dihedral : 15.050 175.295 3212 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.61 % Allowed : 12.93 % Favored : 85.46 % 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: 1.98 (0.15), residues: 1132 sheet: -0.29 (0.90), residues: 37 loop : -0.04 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 131 HIS 0.004 0.001 HIS C 106 PHE 0.020 0.001 PHE B 246 TYR 0.008 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 136 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 1.851 Fit side-chains revert: symmetry clash REVERT: E 77 LYS cc_start: 0.8683 (ttpt) cc_final: 0.8469 (tmtt) REVERT: H 36 GLU cc_start: 0.7548 (tt0) cc_final: 0.7204 (tp30) REVERT: H 76 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7281 (t0) outliers start: 25 outliers final: 14 residues processed: 127 average time/residue: 1.2038 time to fit residues: 175.2947 Evaluate side-chains 123 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.816 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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: 0.8204 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18838 Z= 0.298 Angle : 0.896 44.217 26148 Z= 0.356 Chirality : 0.042 0.260 2517 Planarity : 0.005 0.055 3296 Dihedral : 15.198 171.579 3212 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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: 1.66 (0.20), residues: 1897 helix: 1.91 (0.15), residues: 1120 sheet: -0.28 (0.91), residues: 37 loop : -0.02 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 131 HIS 0.006 0.001 HIS B 100 PHE 0.025 0.001 PHE B 246 TYR 0.011 0.001 TYR B 172 ARG 0.006 0.000 ARG B 384 *********************** 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 131 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.740 Fit side-chains REVERT: E 24 SER cc_start: 0.8707 (t) cc_final: 0.7910 (p) REVERT: E 77 LYS cc_start: 0.8736 (ttpt) cc_final: 0.8505 (tmtt) REVERT: H 76 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7382 (t0) outliers start: 22 outliers final: 17 residues processed: 122 average time/residue: 1.2785 time to fit residues: 177.5728 Evaluate side-chains 124 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 LEU 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 C residue 298 SER 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 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 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: 0.0270 chunk 84 optimal weight: 8.9990 chunk 123 optimal weight: 0.7980 chunk 186 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.7240 ------------------------------------------------------------------------------- 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: 0.8145 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18838 Z= 0.164 Angle : 0.860 44.116 26148 Z= 0.336 Chirality : 0.040 0.256 2517 Planarity : 0.004 0.053 3296 Dihedral : 14.981 173.789 3212 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.22 % Allowed : 13.71 % 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: 1.77 (0.20), residues: 1897 helix: 2.00 (0.15), residues: 1130 sheet: -0.32 (0.91), residues: 37 loop : 0.01 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 131 HIS 0.004 0.001 HIS C 106 PHE 0.021 0.001 PHE B 246 TYR 0.008 0.001 TYR B 172 ARG 0.004 0.000 ARG B 384 ********************** 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 129 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 1.827 Fit side-chains REVERT: E 24 SER cc_start: 0.8671 (t) cc_final: 0.7894 (p) REVERT: E 71 ASN cc_start: 0.8121 (t0) cc_final: 0.7594 (t160) REVERT: E 77 LYS cc_start: 0.8671 (ttpt) cc_final: 0.8443 (tmtt) REVERT: H 36 GLU cc_start: 0.7505 (tt0) cc_final: 0.7254 (tp30) outliers start: 19 outliers final: 13 residues processed: 123 average time/residue: 1.2683 time to fit residues: 178.0006 Evaluate side-chains 118 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 1.914 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.076462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.056437 restraints weight = 45938.041| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.29 r_work: 0.2716 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18838 Z= 0.254 Angle : 0.884 44.214 26148 Z= 0.349 Chirality : 0.041 0.271 2517 Planarity : 0.004 0.055 3296 Dihedral : 15.058 172.345 3212 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.84 % Allowed : 14.03 % 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: 1.73 (0.20), residues: 1897 helix: 1.96 (0.15), residues: 1119 sheet: -0.28 (0.91), residues: 37 loop : 0.01 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 131 HIS 0.006 0.001 HIS B 100 PHE 0.024 0.001 PHE B 246 TYR 0.010 0.001 TYR B 172 ARG 0.004 0.000 ARG B 384 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4633.67 seconds wall clock time: 85 minutes 1.29 seconds (5101.29 seconds total)