Starting phenix.real_space_refine on Fri Dec 8 08:43:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xji_33228/12_2023/7xji_33228_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xji_33228/12_2023/7xji_33228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xji_33228/12_2023/7xji_33228.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xji_33228/12_2023/7xji_33228.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xji_33228/12_2023/7xji_33228_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xji_33228/12_2023/7xji_33228_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 46 5.16 5 Cl 1 4.86 5 C 4977 2.51 5 N 1381 2.21 5 O 1446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "R PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7851 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1884 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2543 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "N" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 950 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2052 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 259} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "G" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 393 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'EI5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.70, per 1000 atoms: 0.60 Number of scatterers: 7851 At special positions: 0 Unit cell: (101.592, 77.688, 132.667, 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) Cl 1 17.00 S 46 16.00 O 1446 8.00 N 1381 7.00 C 4977 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, 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 110 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS R 189 " - pdb=" SG CYS R 195 " distance=2.04 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: 3.03 Conformation dependent library (CDL) restraints added in 1.5 seconds 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 10 sheets defined 35.9% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 10 through 39 removed outlier: 3.513A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 56 No H-bonds generated for 'chain 'A' and resid 53 through 56' Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 284 through 293 Processing helix chain 'A' and resid 298 through 301 No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 322 through 340 removed outlier: 3.553A pdb=" N ILE A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 380 removed outlier: 3.899A pdb=" N ASP A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP A 371 " --> pdb=" O ASN A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 24 removed outlier: 3.683A pdb=" N GLN B 6 " --> pdb=" O SER B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 40 through 63 removed outlier: 3.951A pdb=" N ALA R 50 " --> pdb=" O LEU R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 68 No H-bonds generated for 'chain 'R' and resid 66 through 68' Processing helix chain 'R' and resid 73 through 89 Processing helix chain 'R' and resid 91 through 99 Processing helix chain 'R' and resid 107 through 140 Processing helix chain 'R' and resid 151 through 169 Processing helix chain 'R' and resid 202 through 212 Processing helix chain 'R' and resid 214 through 240 Processing helix chain 'R' and resid 290 through 317 removed outlier: 4.493A pdb=" N CYS R 304 " --> pdb=" O THR R 300 " (cutoff:3.500A) Proline residue: R 307 - end of helix Processing helix chain 'R' and resid 325 through 345 Proline residue: R 343 - end of helix Processing helix chain 'R' and resid 350 through 359 Processing helix chain 'G' and resid 11 through 24 removed outlier: 3.579A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 removed outlier: 3.510A pdb=" N TYR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing sheet with id= A, first strand: chain 'A' and resid 277 through 281 removed outlier: 6.204A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.074A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.677A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.711A 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 150 removed outlier: 7.110A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 191 removed outlier: 6.798A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.984A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 296 through 298 removed outlier: 4.341A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.886A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.531A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.084A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 990 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: 2.09 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2590 1.34 - 1.46: 1911 1.46 - 1.58: 3445 1.58 - 1.70: 0 1.70 - 1.82: 62 Bond restraints: 8008 Sorted by residual: bond pdb=" C6 EI5 R 401 " pdb=" O1 EI5 R 401 " ideal model delta sigma weight residual 1.246 1.306 -0.060 2.00e-02 2.50e+03 8.95e+00 bond pdb=" C4 EI5 R 401 " pdb=" C6 EI5 R 401 " ideal model delta sigma weight residual 1.528 1.488 0.040 2.00e-02 2.50e+03 4.04e+00 bond pdb=" CB PRO R 320 " pdb=" CG PRO R 320 " ideal model delta sigma weight residual 1.492 1.567 -0.075 5.00e-02 4.00e+02 2.26e+00 bond pdb=" CA ASN R 192 " pdb=" CB ASN R 192 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.37e+00 bond pdb=" C16 EI5 R 401 " pdb=" O2 EI5 R 401 " ideal model delta sigma weight residual 1.401 1.423 -0.022 2.00e-02 2.50e+03 1.25e+00 ... (remaining 8003 not shown) Histogram of bond angle deviations from ideal: 100.28 - 107.03: 194 107.03 - 113.78: 4494 113.78 - 120.52: 3151 120.52 - 127.27: 2963 127.27 - 134.01: 85 Bond angle restraints: 10887 Sorted by residual: angle pdb=" N VAL A 357 " pdb=" CA VAL A 357 " pdb=" C VAL A 357 " ideal model delta sigma weight residual 112.43 108.30 4.13 9.20e-01 1.18e+00 2.02e+01 angle pdb=" N VAL R 37 " pdb=" CA VAL R 37 " pdb=" C VAL R 37 " ideal model delta sigma weight residual 113.71 110.07 3.64 9.50e-01 1.11e+00 1.47e+01 angle pdb=" C LEU R 221 " pdb=" N PHE R 222 " pdb=" CA PHE R 222 " ideal model delta sigma weight residual 120.68 114.20 6.48 1.70e+00 3.46e-01 1.45e+01 angle pdb=" CA CYS R 195 " pdb=" CB CYS R 195 " pdb=" SG CYS R 195 " ideal model delta sigma weight residual 114.40 122.04 -7.64 2.30e+00 1.89e-01 1.10e+01 angle pdb=" C VAL R 90 " pdb=" N VAL R 91 " pdb=" CA VAL R 91 " ideal model delta sigma weight residual 120.33 122.49 -2.16 8.00e-01 1.56e+00 7.28e+00 ... (remaining 10882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.75: 4398 19.75 - 39.50: 319 39.50 - 59.25: 38 59.25 - 79.00: 9 79.00 - 98.75: 6 Dihedral angle restraints: 4770 sinusoidal: 1794 harmonic: 2976 Sorted by residual: dihedral pdb=" CB CYS R 110 " pdb=" SG CYS R 110 " pdb=" SG CYS R 196 " pdb=" CB CYS R 196 " ideal model delta sinusoidal sigma weight residual 93.00 -177.52 -89.48 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS R 189 " pdb=" SG CYS R 189 " pdb=" SG CYS R 195 " pdb=" CB CYS R 195 " ideal model delta sinusoidal sigma weight residual 93.00 4.82 88.18 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 147.93 -54.93 1 1.00e+01 1.00e-02 4.08e+01 ... (remaining 4767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 878 0.039 - 0.078: 281 0.078 - 0.117: 85 0.117 - 0.155: 13 0.155 - 0.194: 1 Chirality restraints: 1258 Sorted by residual: chirality pdb=" CB THR A 315 " pdb=" CA THR A 315 " pdb=" OG1 THR A 315 " pdb=" CG2 THR A 315 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CA ILE R 202 " pdb=" N ILE R 202 " pdb=" C ILE R 202 " pdb=" CB ILE R 202 " both_signs ideal model delta sigma weight residual False 2.43 2.29 0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" CA PRO R 320 " pdb=" N PRO R 320 " pdb=" C PRO R 320 " pdb=" CB PRO R 320 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 1255 not shown) Planarity restraints: 1394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 342 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO R 343 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO R 343 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 343 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 341 " 0.013 2.00e-02 2.50e+03 1.31e-02 3.02e+00 pdb=" CG PHE R 341 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE R 341 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE R 341 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE R 341 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 341 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE R 341 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY R 319 " 0.027 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO R 320 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO R 320 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 320 " 0.022 5.00e-02 4.00e+02 ... (remaining 1391 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 266 2.71 - 3.26: 7861 3.26 - 3.81: 12454 3.81 - 4.35: 15335 4.35 - 4.90: 26303 Nonbonded interactions: 62219 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.165 2.440 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.251 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.267 2.440 nonbonded pdb=" O ARG B 314 " pdb=" OG SER B 331 " model vdw 2.278 2.440 nonbonded pdb=" OD2 ASP B 258 " pdb=" NH1 ARG G 27 " model vdw 2.289 2.520 ... (remaining 62214 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: 0.120 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: 1.040 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 24.910 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 : 0.003 0.075 8008 Z= 0.234 Angle : 0.604 8.196 10887 Z= 0.323 Chirality : 0.042 0.194 1258 Planarity : 0.004 0.048 1394 Dihedral : 13.923 98.747 2832 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.27), residues: 1011 helix: 0.90 (0.27), residues: 391 sheet: -0.97 (0.35), residues: 221 loop : -0.61 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 271 HIS 0.002 0.001 HIS B 183 PHE 0.031 0.002 PHE R 341 TYR 0.012 0.001 TYR R 204 ARG 0.008 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.950 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1788 time to fit residues: 43.1263 Evaluate side-chains 126 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.0205 > 50: distance: 63 - 125: 18.078 distance: 66 - 122: 10.520 distance: 79 - 106: 6.067 distance: 82 - 103: 10.128 distance: 92 - 97: 9.771 distance: 97 - 98: 15.721 distance: 97 - 209: 12.700 distance: 98 - 99: 13.556 distance: 98 - 101: 4.757 distance: 99 - 100: 9.220 distance: 99 - 103: 11.603 distance: 100 - 206: 9.661 distance: 101 - 102: 11.574 distance: 103 - 104: 6.257 distance: 104 - 107: 8.144 distance: 105 - 114: 13.498 distance: 107 - 108: 10.407 distance: 108 - 109: 9.500 distance: 109 - 110: 6.471 distance: 110 - 111: 7.173 distance: 111 - 112: 3.264 distance: 111 - 113: 6.610 distance: 114 - 115: 11.158 distance: 114 - 197: 8.113 distance: 115 - 116: 5.382 distance: 115 - 118: 11.893 distance: 116 - 117: 3.677 distance: 116 - 122: 7.348 distance: 118 - 119: 11.692 distance: 119 - 120: 9.966 distance: 119 - 121: 5.624 distance: 122 - 123: 4.077 distance: 123 - 124: 12.554 distance: 123 - 126: 5.162 distance: 124 - 125: 10.609 distance: 124 - 133: 15.574 distance: 127 - 128: 5.811 distance: 127 - 129: 3.270 distance: 128 - 130: 4.986 distance: 129 - 131: 4.861 distance: 131 - 132: 5.722 distance: 133 - 134: 13.870 distance: 134 - 135: 11.500 distance: 134 - 137: 6.032 distance: 135 - 136: 17.166 distance: 135 - 141: 25.466 distance: 137 - 138: 8.743 distance: 138 - 139: 18.396 distance: 138 - 140: 10.892 distance: 141 - 142: 35.726 distance: 142 - 143: 8.136 distance: 142 - 145: 9.273 distance: 143 - 144: 7.551 distance: 143 - 149: 15.187 distance: 145 - 146: 16.869 distance: 146 - 147: 15.531 distance: 146 - 148: 40.583 distance: 149 - 150: 7.441 distance: 150 - 151: 10.570 distance: 150 - 153: 12.007 distance: 151 - 152: 17.148 distance: 151 - 160: 4.446 distance: 153 - 154: 21.378 distance: 154 - 155: 14.050 distance: 155 - 156: 18.597 distance: 156 - 157: 8.125 distance: 157 - 158: 5.111 distance: 157 - 159: 7.075 distance: 160 - 161: 7.317 distance: 161 - 162: 8.124 distance: 161 - 164: 16.077 distance: 162 - 163: 8.016 distance: 162 - 165: 6.591 distance: 165 - 166: 11.857 distance: 166 - 167: 3.566 distance: 166 - 169: 15.285 distance: 167 - 168: 24.799 distance: 167 - 173: 15.340 distance: 169 - 170: 7.043 distance: 170 - 171: 9.216 distance: 170 - 172: 9.942 distance: 173 - 174: 17.367 distance: 174 - 175: 23.655 distance: 174 - 177: 3.748 distance: 175 - 176: 15.700 distance: 175 - 182: 16.387 distance: 177 - 178: 6.506 distance: 178 - 179: 7.400 distance: 179 - 180: 21.345 distance: 179 - 181: 5.736