Starting phenix.real_space_refine on Fri Mar 15 01:56:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srr_25402/03_2024/7srr_25402_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srr_25402/03_2024/7srr_25402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srr_25402/03_2024/7srr_25402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srr_25402/03_2024/7srr_25402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srr_25402/03_2024/7srr_25402_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srr_25402/03_2024/7srr_25402_updated.pdb" } resolution = 2.9 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1944 atoms to isotropic. 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 54 5.16 5 C 5395 2.51 5 N 1411 2.21 5 O 1534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 20": "OD1" <-> "OD2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C ASP 303": "OD1" <-> "OD2" Residue "C ASP 312": "OD1" <-> "OD2" Residue "R TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8394 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1713 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 6, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2518 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 73 Chain: "D" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 363 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1704 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "R" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2096 Unusual residues: {'7LD': 1} Classifications: {'peptide': 274, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 12, 'TRANS': 261, None: 1} Not linked: pdbres="ILE R 395 " pdbres="7LD R 501 " Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 61 Time building chain proxies: 4.79, per 1000 atoms: 0.57 Number of scatterers: 8394 At special positions: 0 Unit cell: (101.521, 117.139, 131.89, 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 54 16.00 O 1534 8.00 N 1411 7.00 C 5395 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 128 " - pdb=" SG CYS R 207 " distance=2.03 Simple disulfide: pdb=" SG CYS R 350 " - pdb=" SG CYS R 353 " 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: 3.14 Conformation dependent library (CDL) restraints added in 1.5 seconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 12 sheets defined 32.2% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'B' and resid 7 through 31 removed outlier: 3.524A pdb=" N ARG B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 146 through 155 Processing helix chain 'B' and resid 160 through 163 No H-bonds generated for 'chain 'B' and resid 160 through 163' Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 184 through 203 Processing helix chain 'B' and resid 224 through 242 Processing helix chain 'C' and resid 4 through 25 removed outlier: 3.579A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 33 No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'D' and resid 11 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'R' and resid 57 through 81 removed outlier: 3.998A pdb=" N MET R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE R 65 " --> pdb=" O ILE R 61 " (cutoff:3.500A) Proline residue: R 67 - end of helix removed outlier: 3.552A pdb=" N ILE R 76 " --> pdb=" O ASN R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 106 removed outlier: 3.610A pdb=" N PHE R 92 " --> pdb=" O ALA R 88 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU R 93 " --> pdb=" O THR R 89 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET R 94 " --> pdb=" O ASN R 90 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER R 95 " --> pdb=" O TYR R 91 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU R 96 " --> pdb=" O PHE R 92 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL R 103 " --> pdb=" O ALA R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 116 Processing helix chain 'R' and resid 128 through 158 removed outlier: 3.794A pdb=" N LEU R 132 " --> pdb=" O CYS R 128 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE R 133 " --> pdb=" O PRO R 129 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER R 150 " --> pdb=" O LEU R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 164 Processing helix chain 'R' and resid 169 through 187 Processing helix chain 'R' and resid 189 through 192 No H-bonds generated for 'chain 'R' and resid 189 through 192' Processing helix chain 'R' and resid 217 through 220 No H-bonds generated for 'chain 'R' and resid 217 through 220' Processing helix chain 'R' and resid 227 through 244 removed outlier: 3.509A pdb=" N ILE R 232 " --> pdb=" O THR R 228 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR R 237 " --> pdb=" O MET R 233 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N HIS R 242 " --> pdb=" O PHE R 238 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA R 243 " --> pdb=" O LEU R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 336 removed outlier: 3.760A pdb=" N ALA R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER R 323 " --> pdb=" O GLU R 319 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY R 327 " --> pdb=" O SER R 323 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET R 336 " --> pdb=" O LEU R 332 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 349 Processing helix chain 'R' and resid 355 through 361 Processing helix chain 'R' and resid 365 through 374 removed outlier: 3.691A pdb=" N SER R 372 " --> pdb=" O ILE R 368 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER R 373 " --> pdb=" O GLY R 369 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLY R 374 " --> pdb=" O TYR R 370 " (cutoff:3.500A) Processing helix chain 'R' and resid 376 through 379 No H-bonds generated for 'chain 'R' and resid 376 through 379' Processing helix chain 'R' and resid 385 through 394 removed outlier: 4.803A pdb=" N ARG R 393 " --> pdb=" O ASP R 389 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR R 394 " --> pdb=" O ALA R 390 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 211 through 215 removed outlier: 7.435A pdb=" N VAL B 139 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N HIS B 214 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 141 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 109 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN B 80 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU B 36 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N HIS B 82 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU B 38 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N PHE B 84 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.101A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.147A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 7.012A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 220 through 222 removed outlier: 3.686A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 232 removed outlier: 6.947A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.565A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.821A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 115 through 117 removed outlier: 5.794A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.629A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 143 through 148 343 hydrogen bonds defined for protein. 993 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: 2.39 Time building geometry restraints manager: 3.42 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: 2674 1.34 - 1.46: 1849 1.46 - 1.58: 3977 1.58 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 8579 Sorted by residual: bond pdb=" C14 7LD R 501 " pdb=" C16 7LD R 501 " ideal model delta sigma weight residual 1.525 1.403 0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" C11 7LD R 501 " pdb=" C9 7LD R 501 " ideal model delta sigma weight residual 1.525 1.406 0.119 2.00e-02 2.50e+03 3.57e+01 bond pdb=" C10 7LD R 501 " pdb=" C14 7LD R 501 " ideal model delta sigma weight residual 1.501 1.398 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C15 7LD R 501 " pdb=" C7 7LD R 501 " ideal model delta sigma weight residual 1.491 1.396 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C3 7LD R 501 " pdb=" C7 7LD R 501 " ideal model delta sigma weight residual 1.414 1.322 0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 8574 not shown) Histogram of bond angle deviations from ideal: 98.38 - 105.51: 139 105.51 - 112.64: 4563 112.64 - 119.78: 2755 119.78 - 126.91: 4121 126.91 - 134.05: 116 Bond angle restraints: 11694 Sorted by residual: angle pdb=" N LYS R 247 " pdb=" CA LYS R 247 " pdb=" C LYS R 247 " ideal model delta sigma weight residual 112.57 104.65 7.92 1.13e+00 7.83e-01 4.91e+01 angle pdb=" N LEU R 244 " pdb=" CA LEU R 244 " pdb=" C LEU R 244 " ideal model delta sigma weight residual 113.23 105.54 7.69 1.24e+00 6.50e-01 3.85e+01 angle pdb=" N GLN R 320 " pdb=" CA GLN R 320 " pdb=" C GLN R 320 " ideal model delta sigma weight residual 113.88 106.26 7.62 1.23e+00 6.61e-01 3.84e+01 angle pdb=" C GLN R 320 " pdb=" CA GLN R 320 " pdb=" CB GLN R 320 " ideal model delta sigma weight residual 109.03 117.62 -8.59 1.62e+00 3.81e-01 2.81e+01 angle pdb=" N GLU R 319 " pdb=" CA GLU R 319 " pdb=" C GLU R 319 " ideal model delta sigma weight residual 113.17 106.59 6.58 1.26e+00 6.30e-01 2.73e+01 ... (remaining 11689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.36: 4927 30.36 - 60.72: 100 60.72 - 91.07: 7 91.07 - 121.43: 0 121.43 - 151.79: 1 Dihedral angle restraints: 5035 sinusoidal: 1793 harmonic: 3242 Sorted by residual: dihedral pdb=" C16 7LD R 501 " pdb=" C17 7LD R 501 " pdb=" N3 7LD R 501 " pdb=" C18 7LD R 501 " ideal model delta sinusoidal sigma weight residual 91.75 -116.46 -151.79 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" CA GLU R 118 " pdb=" C GLU R 118 " pdb=" N ALA R 119 " pdb=" CA ALA R 119 " ideal model delta harmonic sigma weight residual -180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LYS B 73 " pdb=" C LYS B 73 " pdb=" N PHE B 74 " pdb=" CA PHE B 74 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1187 0.065 - 0.131: 172 0.131 - 0.196: 10 0.196 - 0.261: 3 0.261 - 0.326: 3 Chirality restraints: 1375 Sorted by residual: chirality pdb=" C14 7LD R 501 " pdb=" C10 7LD R 501 " pdb=" C13 7LD R 501 " pdb=" C16 7LD R 501 " both_signs ideal model delta sigma weight residual False 2.63 2.30 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CB VAL R 325 " pdb=" CA VAL R 325 " pdb=" CG1 VAL R 325 " pdb=" CG2 VAL R 325 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C11 7LD R 501 " pdb=" C15 7LD R 501 " pdb=" C9 7LD R 501 " pdb=" N2 7LD R 501 " both_signs ideal model delta sigma weight residual False 2.48 2.18 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 1372 not shown) Planarity restraints: 1469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN R 86 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.38e+00 pdb=" C GLN R 86 " -0.050 2.00e-02 2.50e+03 pdb=" O GLN R 86 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR R 87 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 325 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C VAL R 325 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL R 325 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU R 326 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 323 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C SER R 323 " -0.035 2.00e-02 2.50e+03 pdb=" O SER R 323 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS R 324 " 0.012 2.00e-02 2.50e+03 ... (remaining 1466 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 479 2.74 - 3.28: 7877 3.28 - 3.82: 13016 3.82 - 4.36: 15514 4.36 - 4.90: 27794 Nonbonded interactions: 64680 Sorted by model distance: nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.196 2.440 nonbonded pdb=" O ILE R 205 " pdb=" OG1 THR R 206 " model vdw 2.303 2.440 nonbonded pdb=" NE2 GLN C 75 " pdb=" O SER C 98 " model vdw 2.362 2.520 nonbonded pdb=" O SER E 106 " pdb=" OG SER E 106 " model vdw 2.363 2.440 nonbonded pdb=" NH1 ARG E 190 " pdb=" OD2 ASP E 211 " model vdw 2.374 2.520 ... (remaining 64675 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: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 9.740 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 26.280 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 8579 Z= 0.293 Angle : 0.670 8.591 11694 Z= 0.403 Chirality : 0.048 0.326 1375 Planarity : 0.004 0.046 1469 Dihedral : 12.702 151.787 2927 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.12 % Allowed : 0.70 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.15 (0.26), residues: 1101 helix: 0.48 (0.29), residues: 377 sheet: 1.31 (0.33), residues: 275 loop : -0.96 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 121 HIS 0.012 0.002 HIS R 242 PHE 0.018 0.001 PHE R 133 TYR 0.023 0.001 TYR R 87 ARG 0.002 0.000 ARG R 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 0.894 Fit side-chains REVERT: B 199 ASP cc_start: 0.7358 (m-30) cc_final: 0.7092 (m-30) REVERT: C 188 MET cc_start: 0.8901 (mmm) cc_final: 0.8606 (mmm) REVERT: E 34 MET cc_start: 0.8697 (mmm) cc_final: 0.8419 (mmt) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 1.0213 time to fit residues: 178.4879 Evaluate side-chains 148 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.1980 chunk 82 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN C 293 ASN R 318 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8579 Z= 0.218 Angle : 0.531 7.886 11694 Z= 0.277 Chirality : 0.043 0.152 1375 Planarity : 0.004 0.047 1469 Dihedral : 6.892 144.554 1213 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.76 % Allowed : 8.43 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.36 (0.26), residues: 1101 helix: 0.78 (0.29), residues: 372 sheet: 1.34 (0.33), residues: 275 loop : -0.90 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 121 HIS 0.007 0.001 HIS B 209 PHE 0.017 0.001 PHE B 74 TYR 0.009 0.001 TYR E 178 ARG 0.005 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 0.968 Fit side-chains REVERT: B 199 ASP cc_start: 0.7564 (m-30) cc_final: 0.7244 (m-30) REVERT: B 216 THR cc_start: 0.8063 (p) cc_final: 0.7788 (p) REVERT: C 188 MET cc_start: 0.8902 (mmm) cc_final: 0.8675 (mmm) REVERT: C 217 MET cc_start: 0.7796 (pmm) cc_final: 0.7360 (pmm) REVERT: D 38 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7851 (ttp) outliers start: 15 outliers final: 10 residues processed: 162 average time/residue: 1.0444 time to fit residues: 180.9550 Evaluate side-chains 168 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 157 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain R residue 381 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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: 68.9283 > 50: distance: 4 - 28: 17.842 distance: 8 - 36: 22.497 distance: 23 - 28: 20.679 distance: 28 - 29: 18.599 distance: 29 - 30: 14.978 distance: 29 - 32: 13.053 distance: 30 - 31: 29.166 distance: 30 - 36: 29.454 distance: 32 - 33: 35.660 distance: 32 - 34: 55.869 distance: 33 - 35: 15.651 distance: 37 - 38: 23.907 distance: 37 - 40: 20.776 distance: 38 - 39: 34.142 distance: 38 - 44: 22.260 distance: 40 - 41: 27.925 distance: 41 - 42: 52.614 distance: 42 - 43: 39.913 distance: 44 - 45: 7.579 distance: 45 - 46: 15.329 distance: 45 - 48: 4.430 distance: 46 - 47: 36.268 distance: 46 - 55: 13.259 distance: 48 - 49: 29.370 distance: 49 - 50: 11.440 distance: 49 - 51: 9.678 distance: 50 - 52: 7.069 distance: 51 - 53: 11.353 distance: 52 - 54: 9.169 distance: 53 - 54: 7.751 distance: 55 - 56: 47.826 distance: 56 - 59: 19.726 distance: 57 - 58: 34.706 distance: 57 - 60: 16.971 distance: 60 - 61: 35.912 distance: 61 - 62: 25.540 distance: 61 - 64: 39.521 distance: 62 - 63: 14.406 distance: 62 - 65: 7.690 distance: 65 - 66: 13.040 distance: 66 - 67: 19.749 distance: 66 - 69: 15.954 distance: 67 - 68: 31.127 distance: 67 - 73: 30.233 distance: 69 - 70: 52.353 distance: 70 - 71: 39.504 distance: 71 - 72: 28.740 distance: 73 - 74: 36.817 distance: 74 - 75: 35.507 distance: 74 - 77: 47.709 distance: 75 - 76: 21.435 distance: 75 - 87: 21.419 distance: 77 - 78: 12.620 distance: 78 - 79: 14.491 distance: 78 - 80: 10.606 distance: 79 - 81: 8.348 distance: 80 - 82: 11.553 distance: 80 - 83: 14.208 distance: 81 - 82: 8.504 distance: 82 - 84: 11.051 distance: 83 - 85: 13.913 distance: 84 - 86: 12.658 distance: 85 - 86: 11.516 distance: 87 - 88: 13.808 distance: 88 - 89: 26.958 distance: 88 - 91: 32.766 distance: 89 - 90: 36.232 distance: 89 - 94: 21.440 distance: 91 - 92: 15.064 distance: 92 - 93: 40.508 distance: 94 - 95: 29.073 distance: 95 - 96: 35.390 distance: 95 - 98: 10.836 distance: 96 - 97: 8.740 distance: 96 - 102: 30.647 distance: 98 - 99: 14.744 distance: 99 - 100: 32.305 distance: 99 - 101: 22.087 distance: 102 - 103: 15.811 distance: 102 - 108: 32.810 distance: 103 - 104: 28.633 distance: 103 - 106: 25.813 distance: 104 - 105: 17.873 distance: 104 - 109: 28.201 distance: 106 - 107: 14.548 distance: 107 - 108: 57.209