Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 4 14:06:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2z_32268/10_2023/7w2z_32268_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2z_32268/10_2023/7w2z_32268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2z_32268/10_2023/7w2z_32268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2z_32268/10_2023/7w2z_32268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2z_32268/10_2023/7w2z_32268_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2z_32268/10_2023/7w2z_32268_updated.pdb" } resolution = 2.8 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= 0.008 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: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 5812 2.51 5 N 1544 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 20": "OE1" <-> "OE2" Residue "A PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R ARG 75": "NH1" <-> "NH2" Residue "R ARG 102": "NH1" <-> "NH2" Residue "R ARG 107": "NH1" <-> "NH2" Residue "R ARG 141": "NH1" <-> "NH2" Residue "R GLU 185": "OE1" <-> "OE2" Residue "R ARG 243": "NH1" <-> "NH2" Residue "R ARG 244": "NH1" <-> "NH2" Residue "R GLU 291": "OE1" <-> "OE2" Residue "R ARG 336": "NH1" <-> "NH2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "S ARG 98": "NH1" <-> "NH2" Residue "S ARG 148": "NH1" <-> "NH2" Residue "S ARG 206": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "L ARG 15": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 9080 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1691 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 208} Chain breaks: 2 Chain: "R" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2421 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 12, 'TRANS': 288} Chain breaks: 1 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 418 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} 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: "S" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1760 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 141 Unusual residues: {'K4Q': 1} Classifications: {'peptide': 15, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 12, None: 2} Not linked: pdbres="SER L 2 " pdbres="K4Q L 3 " Not linked: pdbres="K4Q L 3 " pdbres="PHE L 4 " Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.12, per 1000 atoms: 0.56 Number of scatterers: 9080 At special positions: 0 Unit cell: (109.512, 119.652, 126.75, 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 61 16.00 O 1663 8.00 N 1544 7.00 C 5812 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 116 " - pdb=" SG CYS R 198 " distance=2.05 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.51 Conformation dependent library (CDL) restraints added in 1.5 seconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 14 sheets defined 31.9% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 removed outlier: 3.554A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.528A pdb=" N PHE A 216 " --> pdb=" O ILE A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 244 through 255 Processing helix chain 'A' and resid 272 through 281 removed outlier: 4.865A pdb=" N GLU A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 311 removed outlier: 4.050A pdb=" N ALA A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.524A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 70 removed outlier: 3.947A pdb=" N ALA R 44 " --> pdb=" O ALA R 40 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL R 56 " --> pdb=" O ALA R 52 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA R 59 " --> pdb=" O VAL R 55 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR R 64 " --> pdb=" O GLY R 60 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET R 65 " --> pdb=" O ASN R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 74 No H-bonds generated for 'chain 'R' and resid 72 through 74' Processing helix chain 'R' and resid 77 through 94 removed outlier: 3.937A pdb=" N PHE R 93 " --> pdb=" O ASP R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 104 removed outlier: 3.539A pdb=" N LEU R 100 " --> pdb=" O MET R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 143 removed outlier: 3.621A pdb=" N GLN R 120 " --> pdb=" O CYS R 116 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR R 128 " --> pdb=" O GLU R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 174 removed outlier: 3.632A pdb=" N PHE R 165 " --> pdb=" O LYS R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 181 removed outlier: 3.668A pdb=" N VAL R 180 " --> pdb=" O PRO R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 207 Processing helix chain 'R' and resid 209 through 239 removed outlier: 3.673A pdb=" N TRP R 215 " --> pdb=" O THR R 211 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE R 219 " --> pdb=" O TRP R 215 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE R 220 " --> pdb=" O VAL R 216 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE R 221 " --> pdb=" O SER R 217 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU R 223 " --> pdb=" O ILE R 219 " (cutoff:3.500A) Proline residue: R 224 - end of helix removed outlier: 3.592A pdb=" N CYS R 227 " --> pdb=" O LEU R 223 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL R 230 " --> pdb=" O PHE R 226 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER R 233 " --> pdb=" O THR R 229 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG R 237 " --> pdb=" O SER R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 280 removed outlier: 3.596A pdb=" N VAL R 269 " --> pdb=" O LEU R 265 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE R 272 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS R 275 " --> pdb=" O ALA R 271 " (cutoff:3.500A) Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 282 through 290 removed outlier: 4.236A pdb=" N PHE R 290 " --> pdb=" O PHE R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 315 removed outlier: 3.668A pdb=" N ASN R 305 " --> pdb=" O SER R 301 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU R 306 " --> pdb=" O GLN R 302 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE R 309 " --> pdb=" O ASN R 305 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU R 311 " --> pdb=" O VAL R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 319 through 322 No H-bonds generated for 'chain 'R' and resid 319 through 322' Processing helix chain 'R' and resid 328 through 338 removed outlier: 3.502A pdb=" N VAL R 332 " --> pdb=" O LYS R 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 21 removed outlier: 4.085A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 removed outlier: 3.542A pdb=" N ALA G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) 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 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 209 through 211 No H-bonds generated for 'chain 'S' and resid 209 through 211' Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.595A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'L' and resid 9 through 13 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.459A pdb=" N ILE A 265 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N HIS A 322 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 267 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'R' and resid 182 through 185 removed outlier: 3.647A pdb=" N ARG R 199 " --> pdb=" O GLY R 183 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= D, first strand: chain 'S' and resid 115 through 117 removed outlier: 3.593A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.963A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'S' and resid 143 through 148 Processing sheet with id= G, first strand: chain 'S' and resid 213 through 219 removed outlier: 3.628A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ARG S 168 " --> pdb=" O PRO S 173 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.745A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.817A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.545A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.990A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.836A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.508A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.489A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 978 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: 2.72 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 2 1.21 - 1.37: 3077 1.37 - 1.52: 3750 1.52 - 1.67: 2359 1.67 - 1.82: 86 Bond restraints: 9274 Sorted by residual: bond pdb=" C08 K4Q L 3 " pdb=" O10 K4Q L 3 " ideal model delta sigma weight residual 1.335 1.062 0.273 2.00e-02 2.50e+03 1.87e+02 bond pdb=" C08 K4Q L 3 " pdb=" O09 K4Q L 3 " ideal model delta sigma weight residual 1.204 1.404 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" CB VAL B 71 " pdb=" CG2 VAL B 71 " ideal model delta sigma weight residual 1.521 1.405 0.116 3.30e-02 9.18e+02 1.24e+01 bond pdb=" C VAL S 12 " pdb=" N GLN S 13 " ideal model delta sigma weight residual 1.329 1.384 -0.055 1.60e-02 3.91e+03 1.19e+01 bond pdb=" C MET R 96 " pdb=" N PRO R 97 " ideal model delta sigma weight residual 1.335 1.377 -0.042 1.36e-02 5.41e+03 9.51e+00 ... (remaining 9269 not shown) Histogram of bond angle deviations from ideal: 84.12 - 97.51: 1 97.51 - 110.90: 3282 110.90 - 124.30: 9061 124.30 - 137.69: 225 137.69 - 151.08: 1 Bond angle restraints: 12570 Sorted by residual: angle pdb=" C07 K4Q L 3 " pdb=" C08 K4Q L 3 " pdb=" O10 K4Q L 3 " ideal model delta sigma weight residual 118.23 84.12 34.11 3.00e+00 1.11e-01 1.29e+02 angle pdb=" O09 K4Q L 3 " pdb=" C08 K4Q L 3 " pdb=" O10 K4Q L 3 " ideal model delta sigma weight residual 117.69 151.08 -33.39 3.00e+00 1.11e-01 1.24e+02 angle pdb=" N VAL R 212 " pdb=" CA VAL R 212 " pdb=" C VAL R 212 " ideal model delta sigma weight residual 111.00 103.44 7.56 1.09e+00 8.42e-01 4.81e+01 angle pdb=" N LYS R 117 " pdb=" CA LYS R 117 " pdb=" C LYS R 117 " ideal model delta sigma weight residual 111.69 104.40 7.29 1.23e+00 6.61e-01 3.51e+01 angle pdb=" N ASN S 182 " pdb=" CA ASN S 182 " pdb=" C ASN S 182 " ideal model delta sigma weight residual 109.15 117.61 -8.46 1.44e+00 4.82e-01 3.45e+01 ... (remaining 12565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.38: 5332 31.38 - 62.75: 129 62.75 - 94.13: 14 94.13 - 125.51: 2 125.51 - 156.88: 1 Dihedral angle restraints: 5478 sinusoidal: 2141 harmonic: 3337 Sorted by residual: dihedral pdb=" CA LEU A 353 " pdb=" C LEU A 353 " pdb=" N TYR A 354 " pdb=" CA TYR A 354 " ideal model delta harmonic sigma weight residual -180.00 -155.08 -24.92 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" C04 K4Q L 3 " pdb=" C05 K4Q L 3 " pdb=" C06 K4Q L 3 " pdb=" C07 K4Q L 3 " ideal model delta sinusoidal sigma weight residual 182.71 25.83 156.88 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" CA PHE A 260 " pdb=" C PHE A 260 " pdb=" N ILE A 261 " pdb=" CA ILE A 261 " ideal model delta harmonic sigma weight residual 180.00 157.80 22.20 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 5475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1285 0.097 - 0.194: 130 0.194 - 0.290: 17 0.290 - 0.387: 2 0.387 - 0.484: 1 Chirality restraints: 1435 Sorted by residual: chirality pdb=" CA MET S 180 " pdb=" N MET S 180 " pdb=" C MET S 180 " pdb=" CB MET S 180 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.86e+00 chirality pdb=" CA LYS A 46 " pdb=" N LYS A 46 " pdb=" C LYS A 46 " pdb=" CB LYS A 46 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA ARG S 179 " pdb=" N ARG S 179 " pdb=" C ARG S 179 " pdb=" CB ARG S 179 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 ... (remaining 1432 not shown) Planarity restraints: 1577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C07 K4Q L 3 " 0.018 2.00e-02 2.50e+03 1.03e-01 1.07e+02 pdb=" C08 K4Q L 3 " -0.173 2.00e-02 2.50e+03 pdb=" O09 K4Q L 3 " 0.069 2.00e-02 2.50e+03 pdb=" O10 K4Q L 3 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG R 107 " -0.100 5.00e-02 4.00e+02 1.50e-01 3.61e+01 pdb=" N PRO R 108 " 0.260 5.00e-02 4.00e+02 pdb=" CA PRO R 108 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO R 108 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 277 " 0.050 5.00e-02 4.00e+02 7.41e-02 8.79e+00 pdb=" N PRO R 278 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO R 278 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 278 " 0.042 5.00e-02 4.00e+02 ... (remaining 1574 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 108 2.64 - 3.21: 7527 3.21 - 3.77: 13450 3.77 - 4.34: 19712 4.34 - 4.90: 32643 Nonbonded interactions: 73440 Sorted by model distance: nonbonded pdb=" O ASN A 43 " pdb=" ND2 ASN A 43 " model vdw 2.078 2.520 nonbonded pdb=" OD2 ASP R 99 " pdb=" OH TYR R 313 " model vdw 2.196 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.228 2.440 nonbonded pdb=" OE2 GLU R 197 " pdb=" OG SER L 6 " model vdw 2.258 2.440 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.290 2.440 ... (remaining 73435 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: 0.310 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: 2.140 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 26.620 Find NCS groups from input model: 0.290 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:12.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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 : 0.009 0.273 9274 Z= 0.600 Angle : 1.133 34.107 12570 Z= 0.608 Chirality : 0.064 0.484 1435 Planarity : 0.009 0.150 1577 Dihedral : 14.533 156.882 3313 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.62 % Favored : 96.29 % Rotamer: Outliers : 0.82 % Allowed : 6.53 % Favored : 92.65 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.78 % 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: -4.01 (0.20), residues: 1132 helix: -4.36 (0.12), residues: 390 sheet: -0.81 (0.28), residues: 295 loop : -2.09 (0.24), residues: 447 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 0.982 Fit side-chains outliers start: 8 outliers final: 1 residues processed: 141 average time/residue: 1.3930 time to fit residues: 208.6382 Evaluate side-chains 107 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.5130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A 312 ASN A 330 ASN R 79 ASN R 196 ASN R 305 ASN R 324 ASN G 11 GLN S 130 GLN B 13 GLN B 32 GLN B 155 ASN B 239 ASN B 340 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9274 Z= 0.196 Angle : 0.564 6.613 12570 Z= 0.298 Chirality : 0.042 0.221 1435 Planarity : 0.006 0.136 1577 Dihedral : 7.606 109.968 1272 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.30 % Favored : 97.61 % Rotamer: Outliers : 3.06 % Allowed : 12.14 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -2.20 (0.22), residues: 1132 helix: -2.04 (0.22), residues: 384 sheet: -0.15 (0.30), residues: 287 loop : -1.63 (0.25), residues: 461 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 105 time to evaluate : 1.058 Fit side-chains outliers start: 30 outliers final: 12 residues processed: 126 average time/residue: 1.2528 time to fit residues: 168.9022 Evaluate side-chains 104 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 1.177 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 4 average time/residue: 0.4011 time to fit residues: 3.3698 ------------------------------------------------------------------------------- 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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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: 70.3573 > 50: distance: 5 - 8: 16.406 distance: 8 - 9: 25.746 distance: 9 - 12: 49.702 distance: 12 - 13: 39.329 distance: 14 - 15: 15.732 distance: 15 - 16: 29.957 distance: 15 - 18: 31.049 distance: 16 - 17: 40.341 distance: 16 - 20: 20.301 distance: 20 - 21: 38.442 distance: 21 - 22: 9.533 distance: 21 - 24: 4.245 distance: 22 - 23: 30.886 distance: 22 - 27: 5.757 distance: 24 - 25: 34.088 distance: 24 - 26: 41.898 distance: 27 - 28: 7.011 distance: 27 - 33: 12.843 distance: 28 - 29: 43.780 distance: 28 - 31: 7.058 distance: 29 - 30: 18.404 distance: 29 - 34: 14.614 distance: 31 - 32: 6.116 distance: 32 - 33: 4.937 distance: 34 - 35: 4.160 distance: 35 - 36: 36.613 distance: 35 - 38: 13.380 distance: 36 - 37: 37.813 distance: 36 - 41: 14.383 distance: 38 - 39: 22.454 distance: 38 - 40: 17.060 distance: 41 - 42: 20.893 distance: 42 - 43: 36.289 distance: 42 - 45: 30.225 distance: 43 - 44: 18.932 distance: 43 - 48: 18.728 distance: 45 - 46: 12.952 distance: 45 - 47: 40.098 distance: 48 - 49: 21.777 distance: 48 - 54: 43.860 distance: 49 - 50: 24.735 distance: 49 - 52: 15.695 distance: 50 - 51: 35.673 distance: 50 - 55: 44.815 distance: 52 - 53: 46.729 distance: 53 - 54: 40.736 distance: 55 - 56: 4.956 distance: 57 - 58: 20.395 distance: 59 - 60: 6.014 distance: 60 - 61: 13.886 distance: 60 - 63: 15.979 distance: 61 - 62: 21.888 distance: 61 - 64: 43.202 distance: 64 - 65: 10.791 distance: 65 - 66: 6.430 distance: 65 - 68: 22.009 distance: 66 - 67: 6.584 distance: 66 - 70: 28.623 distance: 68 - 69: 7.920