Starting phenix.real_space_refine on Fri Mar 15 05:07:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kan_22776/03_2024/7kan_22776_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kan_22776/03_2024/7kan_22776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kan_22776/03_2024/7kan_22776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kan_22776/03_2024/7kan_22776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kan_22776/03_2024/7kan_22776_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kan_22776/03_2024/7kan_22776_trim_updated.pdb" } resolution = 3.7 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= 0.004 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 49 5.16 5 C 6866 2.51 5 N 1790 2.21 5 O 1819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "C ASP 30": "OD1" <-> "OD2" Residue "C ARG 31": "NH1" <-> "NH2" Residue "D ARG 230": "NH1" <-> "NH2" Residue "D ARG 246": "NH1" <-> "NH2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "D ARG 304": "NH1" <-> "NH2" Residue "D ARG 311": "NH1" <-> "NH2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D ARG 368": "NH1" <-> "NH2" Residue "D GLU 396": "OE1" <-> "OE2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D PHE 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 28": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 68": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 93": "NH1" <-> "NH2" Residue "E ASP 110": "OD1" <-> "OD2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 150": "NH1" <-> "NH2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ARG 173": "NH1" <-> "NH2" Residue "F ASP 16": "OD1" <-> "OD2" Residue "F ARG 88": "NH1" <-> "NH2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F ARG 118": "NH1" <-> "NH2" Residue "F GLU 169": "OE1" <-> "OE2" Residue "F ASP 174": "OD1" <-> "OD2" Residue "F GLU 175": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10526 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3331 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 8, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "C" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 440 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 54} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 245 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3612 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 31, 'TRANS': 438} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 78 Chain: "E" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1355 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "F" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1454 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 178} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Time building chain proxies: 6.44, per 1000 atoms: 0.61 Number of scatterers: 10526 At special positions: 0 Unit cell: (107.16, 124.26, 136.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 2 15.00 O 1819 8.00 N 1790 7.00 C 6866 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=0, symmetry=0 Time building additional restraints: 4.47 Conformation dependent library (CDL) restraints added in 2.1 seconds 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2562 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 5 sheets defined 60.6% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 Processing helix chain 'A' and resid 67 through 70 No H-bonds generated for 'chain 'A' and resid 67 through 70' Processing helix chain 'A' and resid 83 through 98 removed outlier: 3.510A pdb=" N SER A 88 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 136 removed outlier: 3.944A pdb=" N LEU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 145 No H-bonds generated for 'chain 'A' and resid 142 through 145' Processing helix chain 'A' and resid 147 through 172 removed outlier: 4.282A pdb=" N VAL A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 160 " --> pdb=" O GLN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.811A pdb=" N ASN A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 224 Processing helix chain 'A' and resid 228 through 235 Processing helix chain 'A' and resid 244 through 262 removed outlier: 4.178A pdb=" N GLY A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 313 removed outlier: 4.029A pdb=" N GLN A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 313 " --> pdb=" O MET A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.535A pdb=" N MET A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 345' Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 358 through 382 removed outlier: 4.259A pdb=" N GLU A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 382 " --> pdb=" O THR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 397 removed outlier: 4.290A pdb=" N LYS A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 438 Proline residue: A 418 - end of helix removed outlier: 3.937A pdb=" N ALA A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 462 removed outlier: 3.608A pdb=" N ILE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 25 Processing helix chain 'C' and resid 31 through 66 Proline residue: C 61 - end of helix Processing helix chain 'B' and resid 96 through 122 removed outlier: 3.652A pdb=" N LEU B 100 " --> pdb=" O PRO B 96 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 32 Proline residue: D 29 - end of helix Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 74 through 96 removed outlier: 4.283A pdb=" N ILE D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ALA D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 202 through 227 removed outlier: 4.421A pdb=" N LEU D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Proline residue: D 218 - end of helix Processing helix chain 'D' and resid 238 through 246 removed outlier: 3.807A pdb=" N ARG D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 261 removed outlier: 3.791A pdb=" N ASN D 259 " --> pdb=" O GLY D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 270 Processing helix chain 'D' and resid 280 through 290 Processing helix chain 'D' and resid 299 through 305 Processing helix chain 'D' and resid 309 through 322 Processing helix chain 'D' and resid 333 through 356 removed outlier: 4.185A pdb=" N GLU D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER D 341 " --> pdb=" O TYR D 337 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER D 345 " --> pdb=" O SER D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 373 Processing helix chain 'D' and resid 383 through 386 removed outlier: 3.635A pdb=" N GLN D 386 " --> pdb=" O PRO D 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 383 through 386' Processing helix chain 'D' and resid 392 through 398 Processing helix chain 'D' and resid 409 through 413 Processing helix chain 'D' and resid 419 through 422 No H-bonds generated for 'chain 'D' and resid 419 through 422' Processing helix chain 'D' and resid 432 through 444 removed outlier: 4.106A pdb=" N SER D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLN D 444 " --> pdb=" O ALA D 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 35 Proline residue: E 9 - end of helix Processing helix chain 'E' and resid 46 through 59 Processing helix chain 'E' and resid 72 through 105 removed outlier: 4.410A pdb=" N GLN E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLN E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARG E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 137 Processing helix chain 'E' and resid 143 through 179 removed outlier: 4.490A pdb=" N THR E 168 " --> pdb=" O GLU E 164 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL E 169 " --> pdb=" O TYR E 165 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ALA E 170 " --> pdb=" O GLN E 166 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLU E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 55 Processing helix chain 'F' and resid 69 through 88 removed outlier: 3.731A pdb=" N ARG F 88 " --> pdb=" O THR F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 106 Processing helix chain 'F' and resid 114 through 135 Processing helix chain 'F' and resid 138 through 151 Processing helix chain 'F' and resid 158 through 170 Processing helix chain 'F' and resid 173 through 186 Processing helix chain 'F' and resid 192 through 202 Processing sheet with id= A, first strand: chain 'A' and resid 264 through 268 removed outlier: 3.507A pdb=" N VAL A 265 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 267 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR A 281 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 269 through 271 Processing sheet with id= C, first strand: chain 'D' and resid 452 through 457 removed outlier: 3.729A pdb=" N LYS D 452 " --> pdb=" O LYS D 474 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 546 through 548 removed outlier: 3.840A pdb=" N ILE D 548 " --> pdb=" O PHE D 563 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 549 through 551 removed outlier: 3.592A pdb=" N GLN D 617 " --> pdb=" O LEU D 603 " (cutoff:3.500A) 595 hydrogen bonds defined for protein. 1773 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1623 1.31 - 1.43: 2765 1.43 - 1.56: 6280 1.56 - 1.68: 4 1.68 - 1.81: 85 Bond restraints: 10757 Sorted by residual: bond pdb=" C21 PC1 A 502 " pdb=" O21 PC1 A 502 " ideal model delta sigma weight residual 1.331 1.404 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C31 PC1 A 501 " pdb=" O31 PC1 A 501 " ideal model delta sigma weight residual 1.330 1.399 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C21 PC1 A 501 " pdb=" O21 PC1 A 501 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C31 PC1 A 502 " pdb=" O31 PC1 A 502 " ideal model delta sigma weight residual 1.330 1.396 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" N PC1 A 502 " pdb=" C12 PC1 A 502 " ideal model delta sigma weight residual 1.500 1.455 0.045 2.00e-02 2.50e+03 4.97e+00 ... (remaining 10752 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.27: 367 106.27 - 113.21: 5958 113.21 - 120.14: 3795 120.14 - 127.07: 4343 127.07 - 134.01: 143 Bond angle restraints: 14606 Sorted by residual: angle pdb=" N PRO D 29 " pdb=" CA PRO D 29 " pdb=" CB PRO D 29 " ideal model delta sigma weight residual 103.25 110.05 -6.80 1.05e+00 9.07e-01 4.19e+01 angle pdb=" C3D PC1 A 501 " pdb=" C3E PC1 A 501 " pdb=" C3F PC1 A 501 " ideal model delta sigma weight residual 113.44 131.90 -18.46 3.00e+00 1.11e-01 3.79e+01 angle pdb=" C3B PC1 A 502 " pdb=" C3C PC1 A 502 " pdb=" C3D PC1 A 502 " ideal model delta sigma weight residual 113.66 131.20 -17.54 3.00e+00 1.11e-01 3.42e+01 angle pdb=" O12 PC1 A 502 " pdb=" P PC1 A 502 " pdb=" O14 PC1 A 502 " ideal model delta sigma weight residual 123.67 109.00 14.67 3.00e+00 1.11e-01 2.39e+01 angle pdb=" O12 PC1 A 501 " pdb=" P PC1 A 501 " pdb=" O14 PC1 A 501 " ideal model delta sigma weight residual 123.67 109.23 14.44 3.00e+00 1.11e-01 2.32e+01 ... (remaining 14601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 5911 17.81 - 35.62: 452 35.62 - 53.43: 81 53.43 - 71.23: 11 71.23 - 89.04: 5 Dihedral angle restraints: 6460 sinusoidal: 2492 harmonic: 3968 Sorted by residual: dihedral pdb=" CA LEU A 80 " pdb=" C LEU A 80 " pdb=" N GLY A 81 " pdb=" CA GLY A 81 " ideal model delta harmonic sigma weight residual -180.00 -155.89 -24.11 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CB GLU D 396 " pdb=" CG GLU D 396 " pdb=" CD GLU D 396 " pdb=" OE1 GLU D 396 " ideal model delta sinusoidal sigma weight residual 0.00 87.35 -87.35 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA THR A 288 " pdb=" C THR A 288 " pdb=" N SER A 289 " pdb=" CA SER A 289 " ideal model delta harmonic sigma weight residual -180.00 -164.63 -15.37 0 5.00e+00 4.00e-02 9.45e+00 ... (remaining 6457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1361 0.045 - 0.091: 278 0.091 - 0.136: 49 0.136 - 0.181: 3 0.181 - 0.227: 2 Chirality restraints: 1693 Sorted by residual: chirality pdb=" CA PRO D 29 " pdb=" N PRO D 29 " pdb=" C PRO D 29 " pdb=" CB PRO D 29 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE D 473 " pdb=" CA ILE D 473 " pdb=" CG1 ILE D 473 " pdb=" CG2 ILE D 473 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ASP D 326 " pdb=" N ASP D 326 " pdb=" C ASP D 326 " pdb=" CB ASP D 326 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.85e-01 ... (remaining 1690 not shown) Planarity restraints: 1820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 277 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" CD GLU D 277 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU D 277 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU D 277 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 56 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO F 57 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 57 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 57 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 292 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" CD GLU D 292 " 0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU D 292 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU D 292 " -0.011 2.00e-02 2.50e+03 ... (remaining 1817 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 874 2.74 - 3.28: 10745 3.28 - 3.82: 16716 3.82 - 4.36: 17140 4.36 - 4.90: 30810 Nonbonded interactions: 76285 Sorted by model distance: nonbonded pdb=" OG1 THR A 419 " pdb=" OD2 ASP C 18 " model vdw 2.197 2.440 nonbonded pdb=" O THR D 464 " pdb=" OG SER D 467 " model vdw 2.242 2.440 nonbonded pdb=" OE1 GLU A 79 " pdb=" OH TYR A 139 " model vdw 2.257 2.440 nonbonded pdb=" NH1 ARG E 159 " pdb=" O ALA F 106 " model vdw 2.285 2.520 nonbonded pdb=" O SER E 37 " pdb=" OG SER E 37 " model vdw 2.299 2.440 ... (remaining 76280 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.930 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 32.310 Find NCS groups from input model: 0.350 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10757 Z= 0.236 Angle : 0.716 18.459 14606 Z= 0.345 Chirality : 0.039 0.227 1693 Planarity : 0.004 0.051 1820 Dihedral : 12.943 89.043 3898 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % 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 (0.22), residues: 1341 helix: -0.20 (0.17), residues: 865 sheet: -2.64 (0.57), residues: 68 loop : -2.69 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 141 HIS 0.003 0.001 HIS B 114 PHE 0.013 0.001 PHE D 15 TYR 0.013 0.001 TYR A 457 ARG 0.002 0.000 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 162 MET cc_start: 0.7946 (tpp) cc_final: 0.7368 (tpp) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2686 time to fit residues: 48.4753 Evaluate side-chains 78 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 10.0000 chunk 102 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 69 optimal weight: 0.0270 chunk 54 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 overall best weight: 1.6844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN D 444 GLN D 470 GLN D 529 GLN E 95 GLN E 114 GLN F 68 ASN F 83 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10757 Z= 0.196 Angle : 0.573 9.049 14606 Z= 0.279 Chirality : 0.037 0.159 1693 Planarity : 0.004 0.047 1820 Dihedral : 7.743 73.516 1553 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.32 % Allowed : 10.96 % Favored : 87.71 % 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: -0.26 (0.23), residues: 1341 helix: 0.88 (0.18), residues: 873 sheet: -2.06 (0.57), residues: 72 loop : -2.16 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP E 141 HIS 0.002 0.001 HIS A 220 PHE 0.015 0.001 PHE D 563 TYR 0.013 0.001 TYR A 64 ARG 0.003 0.000 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 87 LYS cc_start: 0.8303 (ttmm) cc_final: 0.8080 (ttmm) REVERT: E 162 MET cc_start: 0.7945 (tpp) cc_final: 0.7467 (tpp) REVERT: F 174 ASP cc_start: 0.6708 (p0) cc_final: 0.6430 (p0) outliers start: 14 outliers final: 11 residues processed: 96 average time/residue: 0.2093 time to fit residues: 30.0880 Evaluate side-chains 91 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 65 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 102 optimal weight: 0.0010 chunk 83 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 overall best weight: 4.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN F 30 GLN F 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10757 Z= 0.421 Angle : 0.700 12.810 14606 Z= 0.346 Chirality : 0.040 0.162 1693 Planarity : 0.004 0.048 1820 Dihedral : 7.447 64.538 1553 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.27 % Allowed : 16.16 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.24), residues: 1341 helix: 1.21 (0.18), residues: 877 sheet: -1.92 (0.57), residues: 74 loop : -2.12 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 141 HIS 0.004 0.001 HIS F 49 PHE 0.016 0.002 PHE E 42 TYR 0.020 0.002 TYR A 287 ARG 0.003 0.000 ARG D 476 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 75 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASP cc_start: 0.7600 (t0) cc_final: 0.7343 (t0) REVERT: D 270 MET cc_start: 0.7403 (ppp) cc_final: 0.6973 (ppp) REVERT: E 87 LYS cc_start: 0.8414 (ttmm) cc_final: 0.8150 (ttmm) REVERT: E 162 MET cc_start: 0.7938 (tpp) cc_final: 0.7528 (tpp) REVERT: F 174 ASP cc_start: 0.6831 (p0) cc_final: 0.5826 (p0) outliers start: 24 outliers final: 18 residues processed: 93 average time/residue: 0.2052 time to fit residues: 28.6778 Evaluate side-chains 91 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 541 ASP Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 154 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 ASN F 135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10757 Z= 0.295 Angle : 0.616 12.089 14606 Z= 0.302 Chirality : 0.038 0.162 1693 Planarity : 0.004 0.046 1820 Dihedral : 7.151 57.853 1553 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.27 % Allowed : 17.96 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.24), residues: 1341 helix: 1.55 (0.18), residues: 870 sheet: -1.65 (0.59), residues: 72 loop : -1.95 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 141 HIS 0.004 0.001 HIS F 49 PHE 0.013 0.001 PHE E 42 TYR 0.015 0.001 TYR A 287 ARG 0.002 0.000 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 77 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASP cc_start: 0.7693 (t0) cc_final: 0.7386 (t0) REVERT: D 270 MET cc_start: 0.7363 (ppp) cc_final: 0.7056 (ppp) REVERT: E 87 LYS cc_start: 0.8385 (ttmm) cc_final: 0.8140 (ttmm) REVERT: E 162 MET cc_start: 0.7922 (tpp) cc_final: 0.7525 (tpp) REVERT: F 174 ASP cc_start: 0.6605 (p0) cc_final: 0.6121 (p0) outliers start: 24 outliers final: 18 residues processed: 97 average time/residue: 0.2060 time to fit residues: 30.2640 Evaluate side-chains 91 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 541 ASP Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 145 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 117 optimal weight: 8.9990 chunk 32 optimal weight: 0.2980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS F 30 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10757 Z= 0.153 Angle : 0.550 11.238 14606 Z= 0.265 Chirality : 0.036 0.164 1693 Planarity : 0.004 0.044 1820 Dihedral : 6.775 58.453 1553 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.08 % Allowed : 19.94 % Favored : 77.98 % 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: 1.05 (0.24), residues: 1341 helix: 1.88 (0.18), residues: 871 sheet: -1.25 (0.63), residues: 72 loop : -1.67 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 141 HIS 0.003 0.001 HIS C 59 PHE 0.015 0.001 PHE D 15 TYR 0.011 0.001 TYR A 64 ARG 0.003 0.000 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 81 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASP cc_start: 0.7650 (t0) cc_final: 0.7281 (t0) REVERT: E 87 LYS cc_start: 0.8204 (ttmm) cc_final: 0.7969 (ttmm) REVERT: E 162 MET cc_start: 0.7794 (tpp) cc_final: 0.7424 (tpp) REVERT: F 174 ASP cc_start: 0.6583 (p0) cc_final: 0.6109 (p0) outliers start: 22 outliers final: 11 residues processed: 101 average time/residue: 0.2070 time to fit residues: 31.6393 Evaluate side-chains 87 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 541 ASP Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain F residue 65 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 overall best weight: 4.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 604 HIS F 30 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 10757 Z= 0.423 Angle : 0.697 10.882 14606 Z= 0.344 Chirality : 0.040 0.167 1693 Planarity : 0.004 0.048 1820 Dihedral : 7.083 58.211 1553 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.84 % Allowed : 21.08 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.24), residues: 1341 helix: 1.79 (0.18), residues: 869 sheet: -1.29 (0.63), residues: 74 loop : -1.75 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 141 HIS 0.015 0.001 HIS A 133 PHE 0.018 0.002 PHE E 42 TYR 0.015 0.001 TYR A 287 ARG 0.003 0.000 ARG D 476 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 76 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASP cc_start: 0.7776 (t0) cc_final: 0.7440 (t0) REVERT: E 87 LYS cc_start: 0.8432 (ttmm) cc_final: 0.8140 (ttmm) REVERT: E 162 MET cc_start: 0.7940 (tpp) cc_final: 0.7565 (tpp) REVERT: F 174 ASP cc_start: 0.6733 (p0) cc_final: 0.6274 (p0) outliers start: 30 outliers final: 25 residues processed: 99 average time/residue: 0.2112 time to fit residues: 31.2153 Evaluate side-chains 99 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 74 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 541 ASP Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 154 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 130 optimal weight: 0.2980 chunk 81 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 10757 Z= 0.162 Angle : 0.569 10.248 14606 Z= 0.276 Chirality : 0.037 0.171 1693 Planarity : 0.004 0.045 1820 Dihedral : 6.715 57.784 1553 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.80 % Allowed : 21.93 % Favored : 76.28 % 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: 1.30 (0.24), residues: 1341 helix: 2.06 (0.18), residues: 867 sheet: -1.00 (0.65), residues: 72 loop : -1.52 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 141 HIS 0.013 0.001 HIS A 133 PHE 0.014 0.001 PHE D 15 TYR 0.012 0.001 TYR A 287 ARG 0.002 0.000 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASP cc_start: 0.7709 (t0) cc_final: 0.7418 (t0) REVERT: D 270 MET cc_start: 0.7300 (ppp) cc_final: 0.7010 (ppp) REVERT: E 87 LYS cc_start: 0.8338 (ttmm) cc_final: 0.8026 (ttmm) REVERT: E 162 MET cc_start: 0.7747 (tpp) cc_final: 0.7384 (tpp) REVERT: E 168 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8452 (m) REVERT: F 174 ASP cc_start: 0.6686 (p0) cc_final: 0.6296 (p0) outliers start: 19 outliers final: 13 residues processed: 93 average time/residue: 0.1984 time to fit residues: 27.9825 Evaluate side-chains 90 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 541 ASP Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 168 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 102 optimal weight: 0.3980 chunk 118 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN F 135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 10757 Z= 0.279 Angle : 0.609 9.982 14606 Z= 0.296 Chirality : 0.038 0.163 1693 Planarity : 0.004 0.045 1820 Dihedral : 6.790 58.411 1553 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.98 % Allowed : 22.78 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.24), residues: 1341 helix: 2.05 (0.18), residues: 865 sheet: -1.08 (0.64), residues: 74 loop : -1.53 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 141 HIS 0.003 0.001 HIS F 49 PHE 0.013 0.001 PHE E 42 TYR 0.011 0.001 TYR D 435 ARG 0.002 0.000 ARG D 476 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASP cc_start: 0.7757 (t0) cc_final: 0.7464 (t0) REVERT: D 415 MET cc_start: 0.6400 (ppp) cc_final: 0.6125 (ppp) REVERT: E 87 LYS cc_start: 0.8396 (ttmm) cc_final: 0.8081 (ttmm) REVERT: E 162 MET cc_start: 0.7830 (tpp) cc_final: 0.7445 (tpp) REVERT: E 168 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8519 (m) REVERT: F 174 ASP cc_start: 0.6712 (p0) cc_final: 0.6271 (p0) outliers start: 21 outliers final: 19 residues processed: 95 average time/residue: 0.1999 time to fit residues: 29.0747 Evaluate side-chains 96 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 541 ASP Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain F residue 65 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 1.9990 chunk 121 optimal weight: 0.1980 chunk 124 optimal weight: 20.0000 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 0.0070 chunk 95 optimal weight: 0.0670 chunk 37 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 10757 Z= 0.153 Angle : 0.562 9.865 14606 Z= 0.271 Chirality : 0.036 0.164 1693 Planarity : 0.004 0.046 1820 Dihedral : 6.543 59.552 1553 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.51 % Allowed : 22.87 % Favored : 75.61 % 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: 1.40 (0.24), residues: 1341 helix: 2.08 (0.18), residues: 874 sheet: -0.84 (0.66), residues: 72 loop : -1.41 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 141 HIS 0.003 0.001 HIS F 132 PHE 0.015 0.001 PHE D 15 TYR 0.009 0.001 TYR A 287 ARG 0.002 0.000 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASP cc_start: 0.7693 (t0) cc_final: 0.7398 (t0) REVERT: E 87 LYS cc_start: 0.8302 (ttmm) cc_final: 0.8008 (ttmm) REVERT: E 162 MET cc_start: 0.7758 (tpp) cc_final: 0.7376 (tpp) REVERT: E 168 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8401 (m) REVERT: F 174 ASP cc_start: 0.6737 (p0) cc_final: 0.6342 (p0) outliers start: 16 outliers final: 13 residues processed: 92 average time/residue: 0.1989 time to fit residues: 27.9561 Evaluate side-chains 91 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain D residue 541 ASP Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain F residue 65 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 134 optimal weight: 30.0000 chunk 123 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 10757 Z= 0.427 Angle : 0.722 11.059 14606 Z= 0.352 Chirality : 0.040 0.163 1693 Planarity : 0.004 0.047 1820 Dihedral : 6.933 59.543 1553 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.70 % Allowed : 22.97 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.24), residues: 1341 helix: 2.00 (0.18), residues: 868 sheet: -1.03 (0.65), residues: 74 loop : -1.59 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 195 HIS 0.006 0.001 HIS A 133 PHE 0.018 0.002 PHE E 42 TYR 0.018 0.002 TYR D 435 ARG 0.005 0.000 ARG D 419 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.6785 (mmm) cc_final: 0.6578 (tpp) REVERT: A 168 ASP cc_start: 0.7847 (t0) cc_final: 0.7580 (t0) REVERT: D 270 MET cc_start: 0.7204 (ppp) cc_final: 0.6734 (ppp) REVERT: E 87 LYS cc_start: 0.8362 (ttmm) cc_final: 0.8110 (ttmm) REVERT: E 162 MET cc_start: 0.7862 (tpp) cc_final: 0.7494 (tpp) REVERT: E 168 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8505 (m) REVERT: F 174 ASP cc_start: 0.6859 (p0) cc_final: 0.6394 (p0) outliers start: 18 outliers final: 15 residues processed: 93 average time/residue: 0.1952 time to fit residues: 27.5274 Evaluate side-chains 91 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 541 ASP Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 168 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 98 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** 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 = 0.3225 r_free = 0.3225 target = 0.054720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.046760 restraints weight = 60398.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.047967 restraints weight = 31327.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.048643 restraints weight = 20182.822| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 10757 Z= 0.241 Angle : 0.647 13.497 14606 Z= 0.309 Chirality : 0.038 0.164 1693 Planarity : 0.004 0.052 1820 Dihedral : 6.769 59.338 1553 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.51 % Allowed : 23.72 % Favored : 74.76 % 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: 1.33 (0.24), residues: 1341 helix: 2.05 (0.18), residues: 876 sheet: -0.97 (0.65), residues: 74 loop : -1.51 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 141 HIS 0.004 0.001 HIS A 133 PHE 0.011 0.001 PHE E 42 TYR 0.010 0.001 TYR A 52 ARG 0.014 0.000 ARG F 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1764.77 seconds wall clock time: 32 minutes 56.27 seconds (1976.27 seconds total)