Starting phenix.real_space_refine on Tue Jun 25 12:30:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jr9_36593/06_2024/8jr9_36593_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jr9_36593/06_2024/8jr9_36593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jr9_36593/06_2024/8jr9_36593.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jr9_36593/06_2024/8jr9_36593.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jr9_36593/06_2024/8jr9_36593_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jr9_36593/06_2024/8jr9_36593_neut_trim_updated.pdb" } resolution = 2.57 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: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 5027 2.51 5 N 1346 2.21 5 O 1469 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 186": not complete - not flipped Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 7893 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1917 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 227} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2547 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "G" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 389 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "N" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 969 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 123} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "R" Number of atoms: 2071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2071 Unusual residues: {'KHF': 1} Classifications: {'peptide': 255, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 250, None: 1} Not linked: pdbres="LEU R 481 " pdbres="KHF R 601 " Chain breaks: 3 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 6, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 56 Time building chain proxies: 4.76, per 1000 atoms: 0.60 Number of scatterers: 7893 At special positions: 0 Unit cell: (92.288, 108.768, 106.296, 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 48 16.00 F 3 9.00 O 1469 8.00 N 1346 7.00 C 5027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.10 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: 3.06 Conformation dependent library (CDL) restraints added in 1.6 seconds 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 10 sheets defined 38.8% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.007A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 56 removed outlier: 4.516A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 352 removed outlier: 4.317A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'N' and resid 109 through 111 No H-bonds generated for 'chain 'N' and resid 109 through 111' Processing helix chain 'R' and resid 186 through 211 Processing helix chain 'R' and resid 213 through 215 No H-bonds generated for 'chain 'R' and resid 213 through 215' Processing helix chain 'R' and resid 218 through 242 Processing helix chain 'R' and resid 279 through 311 removed outlier: 3.624A pdb=" N ASN R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR R 296 " --> pdb=" O LEU R 292 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 346 Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 357 through 392 removed outlier: 3.579A pdb=" N LYS R 360 " --> pdb=" O GLY R 357 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE R 362 " --> pdb=" O LYS R 359 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE R 363 " --> pdb=" O LYS R 360 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN R 364 " --> pdb=" O TRP R 361 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL R 365 " --> pdb=" O ILE R 362 " (cutoff:3.500A) Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 400 through 413 Processing helix chain 'R' and resid 416 through 427 Processing helix chain 'R' and resid 437 through 459 removed outlier: 4.914A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 464 through 480 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 6.723A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 243 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 224 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLY A 40 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.989A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.778A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.892A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 221 through 223 removed outlier: 4.609A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 263 through 265 removed outlier: 4.599A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.582A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.611A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.577A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.568A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1083 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: 2.25 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1286 1.30 - 1.43: 2203 1.43 - 1.56: 4509 1.56 - 1.68: 1 1.68 - 1.81: 65 Bond restraints: 8064 Sorted by residual: bond pdb=" C16 KHF R 601 " pdb=" N2 KHF R 601 " ideal model delta sigma weight residual 1.274 1.458 -0.184 2.00e-02 2.50e+03 8.46e+01 bond pdb=" C25 KHF R 601 " pdb=" N4 KHF R 601 " ideal model delta sigma weight residual 1.353 1.455 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C12 KHF R 601 " pdb=" C13 KHF R 601 " ideal model delta sigma weight residual 1.530 1.429 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" C13 KHF R 601 " pdb=" C14 KHF R 601 " ideal model delta sigma weight residual 1.532 1.440 0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C TYR B 145 " pdb=" N LEU B 146 " ideal model delta sigma weight residual 1.331 1.275 0.055 1.41e-02 5.03e+03 1.54e+01 ... (remaining 8059 not shown) Histogram of bond angle deviations from ideal: 90.48 - 99.18: 1 99.18 - 107.89: 244 107.89 - 116.59: 5273 116.59 - 125.29: 5299 125.29 - 134.00: 142 Bond angle restraints: 10959 Sorted by residual: angle pdb=" C12 KHF R 601 " pdb=" C13 KHF R 601 " pdb=" N2 KHF R 601 " ideal model delta sigma weight residual 110.89 133.09 -22.20 3.00e+00 1.11e-01 5.48e+01 angle pdb=" C14 KHF R 601 " pdb=" C13 KHF R 601 " pdb=" N2 KHF R 601 " ideal model delta sigma weight residual 110.23 90.48 19.75 3.00e+00 1.11e-01 4.33e+01 angle pdb=" O1 KHF R 601 " pdb=" S1 KHF R 601 " pdb=" O2 KHF R 601 " ideal model delta sigma weight residual 118.72 101.40 17.32 3.00e+00 1.11e-01 3.33e+01 angle pdb=" O TYR B 145 " pdb=" C TYR B 145 " pdb=" N LEU B 146 " ideal model delta sigma weight residual 122.89 116.90 5.99 1.22e+00 6.72e-01 2.41e+01 angle pdb=" N GLN A 294 " pdb=" CA GLN A 294 " pdb=" C GLN A 294 " ideal model delta sigma weight residual 113.23 107.35 5.88 1.24e+00 6.50e-01 2.25e+01 ... (remaining 10954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.08: 4361 25.08 - 50.15: 344 50.15 - 75.23: 38 75.23 - 100.31: 2 100.31 - 125.39: 10 Dihedral angle restraints: 4755 sinusoidal: 1805 harmonic: 2950 Sorted by residual: dihedral pdb=" CA ASP B 186 " pdb=" CB ASP B 186 " pdb=" CG ASP B 186 " pdb=" OD1 ASP B 186 " ideal model delta sinusoidal sigma weight residual 70.00 175.51 -105.51 1 2.00e+01 2.50e-03 3.04e+01 dihedral pdb=" C25 KHF R 601 " pdb=" C27 KHF R 601 " pdb=" N4 KHF R 601 " pdb=" C29 KHF R 601 " ideal model delta sinusoidal sigma weight residual 116.77 -117.84 -125.39 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" C28 KHF R 601 " pdb=" C27 KHF R 601 " pdb=" N4 KHF R 601 " pdb=" C4 KHF R 601 " ideal model delta sinusoidal sigma weight residual -64.48 60.62 -125.10 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 4752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 993 0.045 - 0.090: 181 0.090 - 0.135: 57 0.135 - 0.180: 2 0.180 - 0.225: 4 Chirality restraints: 1237 Sorted by residual: chirality pdb=" CA LEU B 190 " pdb=" N LEU B 190 " pdb=" C LEU B 190 " pdb=" CB LEU B 190 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA VAL R 243 " pdb=" N VAL R 243 " pdb=" C VAL R 243 " pdb=" CB VAL R 243 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1234 not shown) Planarity restraints: 1387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C THR B 87 " -0.030 2.00e-02 2.50e+03 pdb=" O THR B 87 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN B 88 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO A 332 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 145 " 0.007 2.00e-02 2.50e+03 1.30e-02 1.70e+00 pdb=" C TYR B 145 " -0.023 2.00e-02 2.50e+03 pdb=" O TYR B 145 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU B 146 " 0.008 2.00e-02 2.50e+03 ... (remaining 1384 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1474 2.77 - 3.30: 7398 3.30 - 3.84: 13557 3.84 - 4.37: 15177 4.37 - 4.90: 26955 Nonbonded interactions: 64561 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.240 2.440 nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 2.247 2.440 nonbonded pdb=" O VAL R 423 " pdb=" OG1 THR R 427 " model vdw 2.254 2.440 nonbonded pdb=" O THR A 325 " pdb=" OG1 THR A 325 " model vdw 2.260 2.440 nonbonded pdb=" OG SER B 97 " pdb=" OD2 ASP B 118 " model vdw 2.305 2.440 ... (remaining 64556 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 3.580 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.130 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.184 8064 Z= 0.289 Angle : 0.649 22.198 10959 Z= 0.337 Chirality : 0.040 0.225 1237 Planarity : 0.003 0.041 1387 Dihedral : 17.649 125.387 2838 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.24 % Allowed : 24.85 % Favored : 74.91 % 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: 1.80 (0.27), residues: 994 helix: 2.79 (0.26), residues: 400 sheet: 0.86 (0.36), residues: 206 loop : -0.32 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 234 HIS 0.004 0.000 HIS A 387 PHE 0.014 0.001 PHE R 238 TYR 0.009 0.001 TYR R 191 ARG 0.007 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 197 time to evaluate : 0.883 Fit side-chains REVERT: A 14 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6317 (pp20) REVERT: A 15 ARG cc_start: 0.6178 (ttt-90) cc_final: 0.5290 (ttm110) REVERT: A 21 LYS cc_start: 0.7531 (mtpt) cc_final: 0.6548 (tptp) REVERT: A 213 GLN cc_start: 0.7928 (mt0) cc_final: 0.7427 (tt0) REVERT: A 221 MET cc_start: 0.7744 (ptp) cc_final: 0.7421 (ttp) REVERT: A 240 ASP cc_start: 0.5941 (p0) cc_final: 0.5720 (p0) REVERT: A 268 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6501 (tp30) REVERT: A 347 ARG cc_start: 0.7238 (ptp90) cc_final: 0.6813 (ptp-170) REVERT: A 380 ARG cc_start: 0.7733 (ttm110) cc_final: 0.7263 (ttm110) REVERT: A 389 ARG cc_start: 0.7779 (tpp-160) cc_final: 0.7326 (mtm110) REVERT: B 90 VAL cc_start: 0.7823 (m) cc_final: 0.7602 (p) REVERT: B 97 SER cc_start: 0.7018 (p) cc_final: 0.6716 (t) REVERT: B 155 ASN cc_start: 0.6327 (t0) cc_final: 0.6086 (t0) REVERT: B 226 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7037 (mt-10) REVERT: B 325 MET cc_start: 0.8175 (tpp) cc_final: 0.7853 (tpp) REVERT: N 113 THR cc_start: 0.8213 (p) cc_final: 0.7979 (t) REVERT: R 189 MET cc_start: 0.6914 (tpt) cc_final: 0.6519 (tpp) outliers start: 2 outliers final: 1 residues processed: 198 average time/residue: 0.9289 time to fit residues: 197.3692 Evaluate side-chains 126 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 264 ASN A 271 ASN B 75 GLN B 119 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 295 ASN G 44 HIS N 5 GLN N 35 ASN ** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN R 467 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8064 Z= 0.288 Angle : 0.592 6.883 10959 Z= 0.322 Chirality : 0.043 0.142 1237 Planarity : 0.005 0.045 1387 Dihedral : 12.574 126.720 1145 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.75 % Allowed : 20.81 % Favored : 73.44 % 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 (0.27), residues: 994 helix: 2.54 (0.25), residues: 395 sheet: 0.94 (0.33), residues: 223 loop : -0.35 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.011 0.002 HIS A 357 PHE 0.017 0.002 PHE A 363 TYR 0.023 0.002 TYR A 339 ARG 0.006 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 151 time to evaluate : 0.805 Fit side-chains REVERT: A 14 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6517 (pp20) REVERT: A 15 ARG cc_start: 0.6368 (ttt-90) cc_final: 0.5586 (ttp80) REVERT: A 21 LYS cc_start: 0.7561 (mtpt) cc_final: 0.6676 (pptt) REVERT: A 24 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6666 (mp10) REVERT: A 25 LYS cc_start: 0.7859 (ttmm) cc_final: 0.7331 (mttp) REVERT: A 213 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: A 236 GLN cc_start: 0.8763 (mt0) cc_final: 0.8508 (mt0) REVERT: A 240 ASP cc_start: 0.6587 (p0) cc_final: 0.6285 (p0) REVERT: A 370 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7307 (pm20) REVERT: A 389 ARG cc_start: 0.7821 (tpp-160) cc_final: 0.7352 (mtm110) REVERT: A 392 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8192 (mp0) REVERT: B 90 VAL cc_start: 0.7968 (m) cc_final: 0.7631 (p) REVERT: B 142 HIS cc_start: 0.8613 (OUTLIER) cc_final: 0.8139 (m170) REVERT: B 197 ARG cc_start: 0.7179 (tpp-160) cc_final: 0.6376 (mmt90) REVERT: N 70 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8181 (tt) REVERT: N 73 ASP cc_start: 0.7093 (t70) cc_final: 0.6889 (t70) REVERT: R 189 MET cc_start: 0.6924 (tpt) cc_final: 0.6556 (tpp) REVERT: R 207 LEU cc_start: 0.7037 (mt) cc_final: 0.6721 (mm) REVERT: R 286 THR cc_start: 0.7798 (m) cc_final: 0.7431 (m) REVERT: R 312 MET cc_start: 0.6616 (ptp) cc_final: 0.6251 (ptp) REVERT: R 410 THR cc_start: 0.8808 (t) cc_final: 0.8474 (m) outliers start: 47 outliers final: 10 residues processed: 183 average time/residue: 1.0316 time to fit residues: 201.3050 Evaluate side-chains 139 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 61 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 72 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 220 HIS A 264 ASN A 279 ASN A 390 GLN B 259 GLN G 44 HIS R 307 HIS R 364 GLN R 467 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8064 Z= 0.171 Angle : 0.498 7.329 10959 Z= 0.266 Chirality : 0.040 0.150 1237 Planarity : 0.004 0.040 1387 Dihedral : 12.464 127.359 1142 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 4.90 % Allowed : 22.15 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.27), residues: 994 helix: 2.62 (0.25), residues: 394 sheet: 1.11 (0.34), residues: 218 loop : -0.37 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE R 327 TYR 0.013 0.001 TYR R 297 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 129 time to evaluate : 0.901 Fit side-chains REVERT: A 14 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6410 (pp20) REVERT: A 15 ARG cc_start: 0.6330 (ttt-90) cc_final: 0.5575 (ttp80) REVERT: A 21 LYS cc_start: 0.7531 (mtpt) cc_final: 0.6523 (tptp) REVERT: A 24 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6602 (mp10) REVERT: A 213 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: A 236 GLN cc_start: 0.8801 (mt0) cc_final: 0.8557 (mt0) REVERT: A 240 ASP cc_start: 0.6726 (p0) cc_final: 0.6438 (p0) REVERT: A 268 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6543 (tp30) REVERT: A 276 ILE cc_start: 0.8043 (mt) cc_final: 0.7768 (mm) REVERT: A 389 ARG cc_start: 0.7831 (tpp-160) cc_final: 0.7372 (mtm110) REVERT: B 90 VAL cc_start: 0.7845 (m) cc_final: 0.7497 (p) REVERT: B 170 ASP cc_start: 0.7513 (p0) cc_final: 0.7126 (p0) REVERT: B 197 ARG cc_start: 0.7128 (tpp-160) cc_final: 0.6425 (mmt90) REVERT: B 314 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7788 (ptt180) REVERT: N 3 GLN cc_start: 0.7559 (pt0) cc_final: 0.7255 (pt0) REVERT: N 70 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8259 (tt) REVERT: R 189 MET cc_start: 0.6956 (tpt) cc_final: 0.6546 (tpp) REVERT: R 286 THR cc_start: 0.7830 (m) cc_final: 0.7460 (m) REVERT: R 312 MET cc_start: 0.6676 (ptp) cc_final: 0.6338 (ptp) outliers start: 40 outliers final: 15 residues processed: 153 average time/residue: 1.0932 time to fit residues: 178.1053 Evaluate side-chains 142 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 390 ARG Chi-restraints excluded: chain R residue 449 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.0870 chunk 67 optimal weight: 0.0040 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 overall best weight: 0.6170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 213 GLN A 220 HIS A 264 ASN A 390 GLN B 259 GLN G 44 HIS R 307 HIS R 364 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8064 Z= 0.160 Angle : 0.479 6.533 10959 Z= 0.255 Chirality : 0.039 0.150 1237 Planarity : 0.003 0.042 1387 Dihedral : 12.403 127.406 1142 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.53 % Allowed : 22.03 % Favored : 73.44 % 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 (0.27), residues: 994 helix: 2.66 (0.26), residues: 394 sheet: 1.11 (0.33), residues: 213 loop : -0.37 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE R 327 TYR 0.014 0.001 TYR A 358 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 124 time to evaluate : 0.820 Fit side-chains REVERT: A 21 LYS cc_start: 0.7554 (mtpt) cc_final: 0.6578 (tptp) REVERT: A 28 GLN cc_start: 0.7196 (mt0) cc_final: 0.6675 (mm-40) REVERT: A 55 ILE cc_start: 0.6268 (OUTLIER) cc_final: 0.5951 (pt) REVERT: A 213 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: A 236 GLN cc_start: 0.8802 (mt0) cc_final: 0.8557 (mt0) REVERT: A 240 ASP cc_start: 0.6741 (p0) cc_final: 0.6514 (p0) REVERT: A 268 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6579 (tp30) REVERT: A 276 ILE cc_start: 0.8001 (mt) cc_final: 0.7761 (mm) REVERT: A 389 ARG cc_start: 0.7848 (tpp-160) cc_final: 0.7378 (mtm110) REVERT: B 90 VAL cc_start: 0.7843 (m) cc_final: 0.7611 (p) REVERT: B 197 ARG cc_start: 0.7069 (tpp-160) cc_final: 0.6358 (mmt90) REVERT: B 314 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7832 (ptt180) REVERT: N 3 GLN cc_start: 0.7513 (pt0) cc_final: 0.7224 (pt0) REVERT: N 70 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8296 (tt) REVERT: R 189 MET cc_start: 0.6989 (tpt) cc_final: 0.6562 (tpp) REVERT: R 312 MET cc_start: 0.6760 (ptp) cc_final: 0.6403 (ptp) outliers start: 37 outliers final: 16 residues processed: 152 average time/residue: 1.0814 time to fit residues: 175.4850 Evaluate side-chains 139 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 390 ARG Chi-restraints excluded: chain R residue 449 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS A 264 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN G 44 HIS R 307 HIS R 364 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8064 Z= 0.183 Angle : 0.495 6.033 10959 Z= 0.265 Chirality : 0.040 0.141 1237 Planarity : 0.004 0.043 1387 Dihedral : 12.461 127.569 1142 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.16 % Allowed : 22.77 % Favored : 73.07 % 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 (0.26), residues: 994 helix: 2.67 (0.26), residues: 393 sheet: 1.04 (0.33), residues: 215 loop : -0.33 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE R 327 TYR 0.018 0.001 TYR A 358 ARG 0.003 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 125 time to evaluate : 0.837 Fit side-chains REVERT: A 21 LYS cc_start: 0.7598 (mtpt) cc_final: 0.6606 (tptp) REVERT: A 28 GLN cc_start: 0.7197 (mt0) cc_final: 0.6670 (mm-40) REVERT: A 55 ILE cc_start: 0.6297 (OUTLIER) cc_final: 0.6003 (pt) REVERT: A 213 GLN cc_start: 0.8645 (mt0) cc_final: 0.8251 (tt0) REVERT: A 236 GLN cc_start: 0.8795 (mt0) cc_final: 0.8553 (mt0) REVERT: A 268 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6862 (tt0) REVERT: A 276 ILE cc_start: 0.8044 (mt) cc_final: 0.7776 (mm) REVERT: A 370 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7360 (pm20) REVERT: A 374 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7885 (mtt180) REVERT: A 389 ARG cc_start: 0.7856 (tpp-160) cc_final: 0.7378 (mtm110) REVERT: B 170 ASP cc_start: 0.7676 (p0) cc_final: 0.7424 (p0) REVERT: B 196 THR cc_start: 0.7121 (OUTLIER) cc_final: 0.6880 (p) REVERT: B 197 ARG cc_start: 0.7125 (tpp-160) cc_final: 0.6336 (mmt90) REVERT: B 251 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8191 (mtt90) REVERT: B 314 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7785 (ptt180) REVERT: N 3 GLN cc_start: 0.7445 (pt0) cc_final: 0.7161 (pt0) REVERT: N 70 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8286 (tt) REVERT: R 189 MET cc_start: 0.6967 (tpt) cc_final: 0.6562 (tpp) REVERT: R 198 SER cc_start: 0.7586 (OUTLIER) cc_final: 0.7053 (m) REVERT: R 312 MET cc_start: 0.6944 (ptp) cc_final: 0.6584 (ptp) outliers start: 34 outliers final: 11 residues processed: 151 average time/residue: 1.1576 time to fit residues: 186.1582 Evaluate side-chains 139 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 449 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.4522 > 50: distance: 77 - 81: 10.302 distance: 82 - 83: 19.042 distance: 83 - 84: 17.279 distance: 83 - 85: 15.979 distance: 85 - 86: 15.049 distance: 86 - 87: 15.046 distance: 86 - 89: 32.480 distance: 87 - 88: 9.513 distance: 87 - 93: 8.285 distance: 89 - 90: 19.372 distance: 89 - 91: 36.456 distance: 90 - 92: 22.761 distance: 93 - 94: 30.148 distance: 94 - 95: 19.125 distance: 94 - 97: 20.314 distance: 95 - 96: 11.069 distance: 95 - 100: 4.869 distance: 97 - 98: 12.931 distance: 100 - 101: 6.360 distance: 101 - 102: 7.158 distance: 101 - 104: 9.571 distance: 102 - 103: 7.583 distance: 102 - 106: 3.547 distance: 104 - 105: 22.877 distance: 106 - 107: 9.608 distance: 107 - 108: 15.590 distance: 107 - 110: 4.295 distance: 108 - 109: 14.684 distance: 110 - 111: 10.943 distance: 110 - 112: 9.302 distance: 113 - 114: 14.092 distance: 113 - 176: 4.799 distance: 114 - 115: 6.411 distance: 114 - 117: 13.001 distance: 115 - 116: 15.247 distance: 116 - 173: 20.865 distance: 117 - 118: 23.229 distance: 119 - 120: 5.213 distance: 120 - 121: 4.993 distance: 120 - 123: 8.592 distance: 121 - 122: 14.057 distance: 123 - 124: 9.009 distance: 124 - 125: 15.361 distance: 124 - 126: 3.214 distance: 125 - 127: 15.756 distance: 126 - 128: 15.664 distance: 127 - 129: 5.194 distance: 128 - 129: 11.996 distance: 130 - 131: 11.565 distance: 131 - 132: 15.098 distance: 131 - 134: 10.654 distance: 132 - 133: 15.909 distance: 132 - 136: 20.336 distance: 134 - 135: 5.944 distance: 136 - 137: 3.976 distance: 137 - 138: 3.780 distance: 137 - 140: 4.388 distance: 138 - 139: 12.648 distance: 138 - 145: 4.417 distance: 140 - 141: 15.897 distance: 141 - 142: 9.698 distance: 142 - 143: 9.088 distance: 143 - 144: 16.585 distance: 145 - 146: 10.652 distance: 146 - 147: 4.916 distance: 146 - 149: 14.270 distance: 147 - 148: 4.299 distance: 149 - 150: 6.680