Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 15:24:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dw9_30877/04_2023/7dw9_30877_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dw9_30877/04_2023/7dw9_30877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dw9_30877/04_2023/7dw9_30877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dw9_30877/04_2023/7dw9_30877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dw9_30877/04_2023/7dw9_30877_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dw9_30877/04_2023/7dw9_30877_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 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: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 6423 2.51 5 N 1757 2.21 5 O 1858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 10105 Number of models: 1 Model: "" Number of chains: 8 Chain: "R" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2177 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 263} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1971 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 2 Chain: "B" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2605 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "S" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1787 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Unusual residues: {'NH2': 1} Classifications: {'peptide': 9, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 1, 'TRANS': 7} Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.78, per 1000 atoms: 0.57 Number of scatterers: 10105 At special positions: 0 Unit cell: (131.88, 89.04, 118.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 1858 8.00 N 1757 7.00 C 6423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 112 " - pdb=" SG CYS R 192 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS C 1 " - pdb=" SG CYS C 6 " distance=2.03 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: 4.50 Conformation dependent library (CDL) restraints added in 1.6 seconds 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 15 sheets defined 32.2% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'R' and resid 34 through 66 removed outlier: 4.586A pdb=" N ALA R 39 " --> pdb=" O LEU R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 91 Processing helix chain 'R' and resid 93 through 101 Processing helix chain 'R' and resid 109 through 142 removed outlier: 4.242A pdb=" N ALA R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET R 120 " --> pdb=" O LYS R 116 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N MET R 123 " --> pdb=" O GLN R 119 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR R 124 " --> pdb=" O MET R 120 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE R 130 " --> pdb=" O SER R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 177 removed outlier: 3.591A pdb=" N SER R 171 " --> pdb=" O SER R 167 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU R 172 " --> pdb=" O LEU R 168 " (cutoff:3.500A) Proline residue: R 173 - end of helix removed outlier: 4.229A pdb=" N PHE R 176 " --> pdb=" O LEU R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 213 removed outlier: 3.948A pdb=" N TYR R 205 " --> pdb=" O GLY R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 234 Processing helix chain 'R' and resid 264 through 296 Proline residue: R 286 - end of helix Processing helix chain 'R' and resid 305 through 328 removed outlier: 3.913A pdb=" N LEU R 312 " --> pdb=" O VAL R 308 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU R 313 " --> pdb=" O LEU R 309 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ALA R 314 " --> pdb=" O LEU R 310 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER R 315 " --> pdb=" O MET R 311 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU R 316 " --> pdb=" O LEU R 312 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN R 317 " --> pdb=" O LEU R 313 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N SER R 318 " --> pdb=" O ALA R 314 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS R 319 " --> pdb=" O SER R 315 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR R 320 " --> pdb=" O LEU R 316 " (cutoff:3.500A) Proline residue: R 322 - end of helix Processing helix chain 'R' and resid 330 through 337 removed outlier: 3.762A pdb=" N GLU R 335 " --> pdb=" O SER R 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 38 removed outlier: 4.068A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.598A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 390 removed outlier: 3.889A pdb=" N ALA A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.555A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 24 Processing helix chain 'Y' and resid 30 through 43 Processing helix chain 'Y' and resid 45 through 47 No H-bonds generated for 'chain 'Y' and resid 45 through 47' Processing helix chain 'Y' and resid 56 through 58 No H-bonds generated for 'chain 'Y' and resid 56 through 58' 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 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 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'R' and resid 178 through 181 Processing sheet with id= B, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.294A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.068A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.882A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.781A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.856A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.679A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.546A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.678A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.607A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.154A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= M, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.148A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 140 through 142 Processing sheet with id= O, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.597A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1137 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: 3.10 Time building geometry restraints manager: 4.78 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: 3287 1.34 - 1.46: 2513 1.46 - 1.58: 4436 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 10332 Sorted by residual: bond pdb=" N GLU B 3 " pdb=" CA GLU B 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N THR Y 6 " pdb=" CA THR Y 6 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N CYS A 3 " pdb=" CA CYS A 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N THR R 31 " pdb=" CA THR R 31 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.74e+00 bond pdb=" N CYS C 1 " pdb=" CA CYS C 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.55e+00 ... (remaining 10327 not shown) Histogram of bond angle deviations from ideal: 98.74 - 105.80: 220 105.80 - 112.86: 5403 112.86 - 119.91: 3574 119.91 - 126.97: 4691 126.97 - 134.03: 138 Bond angle restraints: 14026 Sorted by residual: angle pdb=" C14 CLR R 601 " pdb=" C8 CLR R 601 " pdb=" C7 CLR R 601 " ideal model delta sigma weight residual 110.19 122.27 -12.08 3.00e+00 1.11e-01 1.62e+01 angle pdb=" C14 CLR R 602 " pdb=" C8 CLR R 602 " pdb=" C7 CLR R 602 " ideal model delta sigma weight residual 110.19 122.20 -12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" C14 CLR R 603 " pdb=" C8 CLR R 603 " pdb=" C7 CLR R 603 " ideal model delta sigma weight residual 110.19 121.54 -11.35 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C7 CLR R 603 " pdb=" C8 CLR R 603 " pdb=" C9 CLR R 603 " ideal model delta sigma weight residual 110.39 119.43 -9.04 3.00e+00 1.11e-01 9.07e+00 angle pdb=" N MET S 192 " pdb=" CA MET S 192 " pdb=" C MET S 192 " ideal model delta sigma weight residual 110.80 117.14 -6.34 2.13e+00 2.20e-01 8.87e+00 ... (remaining 14021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5740 17.86 - 35.72: 306 35.72 - 53.58: 40 53.58 - 71.44: 13 71.44 - 89.30: 9 Dihedral angle restraints: 6108 sinusoidal: 2394 harmonic: 3714 Sorted by residual: dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 150.93 29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA PHE B 292 " pdb=" C PHE B 292 " pdb=" N ASN B 293 " pdb=" CA ASN B 293 " ideal model delta harmonic sigma weight residual 180.00 150.97 29.03 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA CYS C 1 " pdb=" C CYS C 1 " pdb=" N TYR C 2 " pdb=" CA TYR C 2 " ideal model delta harmonic sigma weight residual -180.00 -151.42 -28.58 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 6105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.389: 1571 0.389 - 0.778: 0 0.778 - 1.167: 0 1.167 - 1.556: 0 1.556 - 1.945: 3 Chirality restraints: 1574 Sorted by residual: chirality pdb=" C8 CLR R 602 " pdb=" C14 CLR R 602 " pdb=" C7 CLR R 602 " pdb=" C9 CLR R 602 " both_signs ideal model delta sigma weight residual False 2.69 0.75 1.95 2.00e-01 2.50e+01 9.46e+01 chirality pdb=" C8 CLR R 603 " pdb=" C14 CLR R 603 " pdb=" C7 CLR R 603 " pdb=" C9 CLR R 603 " both_signs ideal model delta sigma weight residual False 2.69 0.77 1.93 2.00e-01 2.50e+01 9.26e+01 chirality pdb=" C8 CLR R 601 " pdb=" C14 CLR R 601 " pdb=" C7 CLR R 601 " pdb=" C9 CLR R 601 " both_signs ideal model delta sigma weight residual False 2.69 0.80 1.89 2.00e-01 2.50e+01 8.93e+01 ... (remaining 1571 not shown) Planarity restraints: 1772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 137 " 0.268 9.50e-02 1.11e+02 1.21e-01 1.06e+01 pdb=" NE ARG B 137 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG B 137 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG B 137 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 137 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 150 " 0.257 9.50e-02 1.11e+02 1.15e-01 8.47e+00 pdb=" NE ARG B 150 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 150 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 150 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 150 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP S 47 " -0.002 2.00e-02 2.50e+03 1.70e-02 7.25e+00 pdb=" CG TRP S 47 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP S 47 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP S 47 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP S 47 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TRP S 47 " 0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP S 47 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 47 " 0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 47 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP S 47 " 0.006 2.00e-02 2.50e+03 ... (remaining 1769 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2993 2.83 - 3.34: 9589 3.34 - 3.86: 16058 3.86 - 4.38: 19629 4.38 - 4.90: 33736 Nonbonded interactions: 82005 Sorted by model distance: nonbonded pdb=" O GLY S 9 " pdb=" NH1 ARG S 18 " model vdw 2.306 2.520 nonbonded pdb=" OE1 GLU R 40 " pdb=" NZ LYS R 100 " model vdw 2.322 2.520 nonbonded pdb=" OG1 THR N 28 " pdb=" OD1 ASN N 31 " model vdw 2.354 2.440 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.356 2.440 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.362 2.440 ... (remaining 82000 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 2.250 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 29.850 Find NCS groups from input model: 0.290 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: 0.010 Load rotamer database and sin/cos tables:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 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 : 0.006 0.052 10332 Z= 0.402 Angle : 0.771 12.081 14026 Z= 0.428 Chirality : 0.097 1.945 1574 Planarity : 0.009 0.121 1772 Dihedral : 12.061 89.296 3697 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -0.01 (0.22), residues: 1259 helix: -0.18 (0.24), residues: 395 sheet: 0.67 (0.26), residues: 340 loop : -0.15 (0.26), residues: 524 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 182 average time/residue: 1.6724 time to fit residues: 321.0165 Evaluate side-chains 134 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 1.5954 time to fit residues: 3.3051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 30.0000 chunk 97 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 293 ASN N 3 GLN S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 10332 Z= 0.290 Angle : 0.643 6.928 14026 Z= 0.343 Chirality : 0.045 0.202 1574 Planarity : 0.005 0.034 1772 Dihedral : 5.671 47.067 1431 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.01 (0.23), residues: 1259 helix: 1.36 (0.26), residues: 400 sheet: 0.86 (0.27), residues: 328 loop : 0.13 (0.27), residues: 531 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 1.269 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 156 average time/residue: 1.6115 time to fit residues: 266.2218 Evaluate side-chains 134 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 130 time to evaluate : 1.267 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1677 time to fit residues: 2.6450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/iotbx/cli_parser.py", line 870, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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: 52.9171 > 50: distance: 24 - 29: 18.828 distance: 29 - 30: 30.323 distance: 30 - 31: 13.421 distance: 31 - 32: 17.618 distance: 31 - 33: 15.449 distance: 33 - 34: 45.790 distance: 34 - 35: 5.387 distance: 34 - 37: 24.471 distance: 35 - 36: 36.948 distance: 35 - 38: 20.214 distance: 38 - 39: 22.405 distance: 39 - 40: 24.122 distance: 39 - 42: 33.639 distance: 40 - 41: 20.118 distance: 40 - 47: 37.074 distance: 42 - 43: 18.990 distance: 43 - 44: 11.359 distance: 44 - 45: 28.128 distance: 44 - 46: 31.382 distance: 47 - 48: 12.810 distance: 48 - 49: 32.609 distance: 48 - 51: 14.481 distance: 49 - 50: 33.360 distance: 49 - 58: 34.732 distance: 51 - 52: 50.545 distance: 52 - 53: 27.832 distance: 53 - 54: 11.902 distance: 54 - 55: 15.786 distance: 55 - 56: 11.680 distance: 55 - 57: 7.473 distance: 58 - 59: 12.326 distance: 59 - 60: 19.969 distance: 59 - 62: 17.936 distance: 60 - 61: 16.716 distance: 60 - 66: 9.391 distance: 62 - 63: 9.077 distance: 63 - 64: 5.077 distance: 63 - 65: 9.378 distance: 66 - 67: 9.958 distance: 67 - 68: 19.988 distance: 67 - 70: 21.526 distance: 68 - 69: 12.102 distance: 68 - 75: 32.805 distance: 70 - 71: 31.851 distance: 71 - 72: 8.268 distance: 72 - 73: 22.700 distance: 72 - 74: 15.477 distance: 75 - 76: 11.971 distance: 76 - 77: 26.899 distance: 76 - 79: 22.611 distance: 77 - 78: 18.303 distance: 77 - 86: 10.416 distance: 79 - 80: 30.750 distance: 80 - 81: 26.773 distance: 81 - 82: 5.187 distance: 82 - 83: 12.801 distance: 83 - 84: 9.964 distance: 83 - 85: 10.490 distance: 86 - 87: 11.664 distance: 87 - 88: 9.922 distance: 87 - 90: 10.929 distance: 88 - 89: 21.784 distance: 88 - 97: 9.822 distance: 90 - 91: 21.563 distance: 91 - 92: 12.959 distance: 92 - 93: 4.471 distance: 93 - 94: 6.865 distance: 97 - 98: 15.008 distance: 98 - 99: 18.215 distance: 98 - 101: 15.381 distance: 99 - 100: 30.318 distance: 99 - 106: 17.594 distance: 101 - 102: 10.716 distance: 102 - 103: 7.334 distance: 103 - 104: 15.645 distance: 104 - 105: 17.532 distance: 106 - 107: 7.835 distance: 107 - 108: 10.466 distance: 107 - 110: 8.507 distance: 108 - 109: 10.391 distance: 108 - 120: 3.387 distance: 109 - 136: 15.801 distance: 110 - 111: 10.696 distance: 111 - 112: 7.170 distance: 111 - 113: 4.689 distance: 112 - 114: 5.590 distance: 113 - 115: 6.479 distance: 113 - 116: 3.690 distance: 114 - 115: 3.247 distance: 115 - 117: 8.785 distance: 116 - 118: 8.706 distance: 117 - 119: 5.849 distance: 118 - 119: 4.460