Starting phenix.real_space_refine on Fri Dec 8 18:57:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vms_21243/12_2023/6vms_21243_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vms_21243/12_2023/6vms_21243.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vms_21243/12_2023/6vms_21243_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vms_21243/12_2023/6vms_21243_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vms_21243/12_2023/6vms_21243_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vms_21243/12_2023/6vms_21243.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vms_21243/12_2023/6vms_21243.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vms_21243/12_2023/6vms_21243_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vms_21243/12_2023/6vms_21243_updated.pdb" } resolution = 3.8 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= 0.003 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: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 65 5.16 5 C 5705 2.51 5 N 1512 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 43": "OE1" <-> "OE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 74": "OD1" <-> "OD2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E ASP 223": "OD1" <-> "OD2" Residue "E GLU 246": "OE1" <-> "OE2" Residue "R GLU 99": "OE1" <-> "OE2" Residue "R ASP 400": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8953 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1823 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 224} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 454 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "E" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1782 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2287 Unusual residues: {'08Y': 1} Classifications: {'peptide': 278, 'undetermined': 1} Link IDs: {'PTRANS': 9, 'TRANS': 268, None: 1} Not linked: pdbres="CYS R 443 " pdbres="08Y R 601 " Time building chain proxies: 5.13, per 1000 atoms: 0.57 Number of scatterers: 8953 At special positions: 0 Unit cell: (103.75, 117.86, 128.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 65 16.00 O 1670 8.00 N 1512 7.00 C 5705 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 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS R 399 " - pdb=" SG CYS R 401 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.55 Conformation dependent library (CDL) restraints added in 1.8 seconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 13 sheets defined 34.5% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.618A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 208 through 215 removed outlier: 5.194A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 274 through 280 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.977A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.806A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.224A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 23 removed outlier: 4.114A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'R' and resid 36 through 61 removed outlier: 3.515A pdb=" N LEU R 40 " --> pdb=" O TYR R 37 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE R 48 " --> pdb=" O ILE R 45 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN R 52 " --> pdb=" O VAL R 49 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL R 53 " --> pdb=" O PHE R 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU R 54 " --> pdb=" O GLY R 51 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL R 55 " --> pdb=" O ASN R 52 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N CYS R 56 " --> pdb=" O VAL R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 86 Processing helix chain 'R' and resid 88 through 96 Processing helix chain 'R' and resid 106 through 137 Processing helix chain 'R' and resid 145 through 170 removed outlier: 3.670A pdb=" N LYS R 149 " --> pdb=" O ARG R 145 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ARG R 150 " --> pdb=" O TYR R 146 " (cutoff:3.500A) Proline residue: R 169 - end of helix Processing helix chain 'R' and resid 187 through 197 removed outlier: 4.329A pdb=" N ILE R 195 " --> pdb=" O VAL R 191 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL R 196 " --> pdb=" O TYR R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 222 Processing helix chain 'R' and resid 364 through 398 removed outlier: 3.526A pdb=" N LYS R 369 " --> pdb=" O GLN R 365 " (cutoff:3.500A) Proline residue: R 388 - end of helix removed outlier: 3.609A pdb=" N ILE R 397 " --> pdb=" O HIS R 393 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS R 398 " --> pdb=" O ILE R 394 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 425 removed outlier: 3.872A pdb=" N ALA R 410 " --> pdb=" O VAL R 406 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN R 418 " --> pdb=" O LEU R 414 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER R 419 " --> pdb=" O GLY R 415 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA R 420 " --> pdb=" O TYR R 416 " (cutoff:3.500A) Proline residue: R 423 - end of helix Processing helix chain 'R' and resid 431 through 440 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.563A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.985A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.924A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.800A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.070A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.804A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.563A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 318 through 320 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 10 through 12 removed outlier: 5.440A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 140 through 142 Processing sheet with id= L, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.530A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 225 through 231 removed outlier: 6.413A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1095 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: 3.00 Time building geometry restraints manager: 3.81 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: 2875 1.34 - 1.47: 2292 1.47 - 1.60: 3880 1.60 - 1.73: 0 1.73 - 1.86: 94 Bond restraints: 9141 Sorted by residual: bond pdb=" C16 08Y R 601 " pdb=" C22 08Y R 601 " ideal model delta sigma weight residual 0.960 1.502 -0.542 2.00e-02 2.50e+03 7.34e+02 bond pdb=" C16 08Y R 601 " pdb=" C18 08Y R 601 " ideal model delta sigma weight residual 2.019 1.524 0.495 2.00e-02 2.50e+03 6.13e+02 bond pdb=" C21 08Y R 601 " pdb=" C22 08Y R 601 " ideal model delta sigma weight residual 1.794 1.333 0.461 2.00e-02 2.50e+03 5.32e+02 bond pdb=" C17 08Y R 601 " pdb=" C21 08Y R 601 " ideal model delta sigma weight residual 1.139 1.535 -0.396 2.00e-02 2.50e+03 3.93e+02 bond pdb=" C17 08Y R 601 " pdb=" N4 08Y R 601 " ideal model delta sigma weight residual 1.814 1.481 0.333 2.00e-02 2.50e+03 2.78e+02 ... (remaining 9136 not shown) Histogram of bond angle deviations from ideal: 99.14 - 107.26: 259 107.26 - 115.37: 5631 115.37 - 123.49: 6150 123.49 - 131.61: 340 131.61 - 139.73: 21 Bond angle restraints: 12401 Sorted by residual: angle pdb=" C23 08Y R 601 " pdb=" C25 08Y R 601 " pdb=" C29 08Y R 601 " ideal model delta sigma weight residual 120.93 139.73 -18.80 3.00e+00 1.11e-01 3.93e+01 angle pdb=" C1 08Y R 601 " pdb=" N2 08Y R 601 " pdb=" C9 08Y R 601 " ideal model delta sigma weight residual 110.69 127.75 -17.06 3.00e+00 1.11e-01 3.23e+01 angle pdb=" C16 08Y R 601 " pdb=" C22 08Y R 601 " pdb=" C21 08Y R 601 " ideal model delta sigma weight residual 108.42 123.59 -15.17 3.00e+00 1.11e-01 2.56e+01 angle pdb=" C6 08Y R 601 " pdb=" N2 08Y R 601 " pdb=" C9 08Y R 601 " ideal model delta sigma weight residual 137.12 122.36 14.76 3.00e+00 1.11e-01 2.42e+01 angle pdb=" C3 08Y R 601 " pdb=" N1 08Y R 601 " pdb=" C8 08Y R 601 " ideal model delta sigma weight residual 138.85 126.43 12.42 3.00e+00 1.11e-01 1.71e+01 ... (remaining 12396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 5191 17.47 - 34.94: 186 34.94 - 52.41: 43 52.41 - 69.88: 19 69.88 - 87.35: 6 Dihedral angle restraints: 5445 sinusoidal: 2134 harmonic: 3311 Sorted by residual: dihedral pdb=" CB CYS R 399 " pdb=" SG CYS R 399 " pdb=" SG CYS R 401 " pdb=" CB CYS R 401 " ideal model delta sinusoidal sigma weight residual -86.00 -145.68 59.68 1 1.00e+01 1.00e-02 4.75e+01 dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 149.27 -56.27 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CA PRO R 139 " pdb=" C PRO R 139 " pdb=" N MET R 140 " pdb=" CA MET R 140 " ideal model delta harmonic sigma weight residual 180.00 157.66 22.34 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 5442 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 941 0.038 - 0.076: 351 0.076 - 0.115: 109 0.115 - 0.153: 16 0.153 - 0.191: 2 Chirality restraints: 1419 Sorted by residual: chirality pdb=" C5 08Y R 601 " pdb=" C11 08Y R 601 " pdb=" C8 08Y R 601 " pdb=" O1 08Y R 601 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.14e-01 chirality pdb=" C17 08Y R 601 " pdb=" C21 08Y R 601 " pdb=" C23 08Y R 601 " pdb=" N4 08Y R 601 " both_signs ideal model delta sigma weight residual False -2.58 -2.42 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA ILE A 221 " pdb=" N ILE A 221 " pdb=" C ILE A 221 " pdb=" CB ILE A 221 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 1416 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C21 08Y R 601 " -0.099 2.00e-02 2.50e+03 8.71e-02 2.28e+02 pdb=" C23 08Y R 601 " 0.157 2.00e-02 2.50e+03 pdb=" C24 08Y R 601 " -0.063 2.00e-02 2.50e+03 pdb=" C25 08Y R 601 " -0.032 2.00e-02 2.50e+03 pdb=" C26 08Y R 601 " -0.107 2.00e-02 2.50e+03 pdb=" C28 08Y R 601 " -0.087 2.00e-02 2.50e+03 pdb=" C29 08Y R 601 " -0.021 2.00e-02 2.50e+03 pdb=" C30 08Y R 601 " 0.092 2.00e-02 2.50e+03 pdb=" C31 08Y R 601 " 0.023 2.00e-02 2.50e+03 pdb=" C32 08Y R 601 " 0.122 2.00e-02 2.50e+03 pdb=" N5 08Y R 601 " -0.056 2.00e-02 2.50e+03 pdb="BR 08Y R 601 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 08Y R 601 " 0.060 2.00e-02 2.50e+03 5.54e-02 4.61e+01 pdb=" C3 08Y R 601 " -0.071 2.00e-02 2.50e+03 pdb=" C6 08Y R 601 " -0.074 2.00e-02 2.50e+03 pdb=" C9 08Y R 601 " 0.008 2.00e-02 2.50e+03 pdb=" N2 08Y R 601 " 0.011 2.00e-02 2.50e+03 pdb=" O4 08Y R 601 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 08Y R 601 " -0.067 2.00e-02 2.50e+03 4.51e-02 3.05e+01 pdb=" C3 08Y R 601 " 0.035 2.00e-02 2.50e+03 pdb=" C5 08Y R 601 " 0.055 2.00e-02 2.50e+03 pdb=" C8 08Y R 601 " -0.000 2.00e-02 2.50e+03 pdb=" N1 08Y R 601 " 0.028 2.00e-02 2.50e+03 pdb=" O3 08Y R 601 " -0.051 2.00e-02 2.50e+03 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 118 2.65 - 3.21: 8357 3.21 - 3.77: 13399 3.77 - 4.34: 19284 4.34 - 4.90: 31092 Nonbonded interactions: 72250 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.082 2.440 nonbonded pdb=" O ALA A 41 " pdb=" OG SER A 44 " model vdw 2.103 2.440 nonbonded pdb=" O SER E 30 " pdb=" OG SER E 53 " model vdw 2.116 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.126 2.440 nonbonded pdb=" OG SER E 106 " pdb=" OH TYR E 190 " model vdw 2.227 2.440 ... (remaining 72245 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.000 Extract box with map and model: 5.950 Check model and map are aligned: 0.000 Set scattering table: 2.120 Process input model: 26.080 Find NCS groups from input model: 0.270 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 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 : 0.013 0.542 9141 Z= 0.912 Angle : 0.826 18.799 12401 Z= 0.419 Chirality : 0.044 0.191 1419 Planarity : 0.005 0.087 1557 Dihedral : 11.208 87.351 3295 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.27 (0.24), residues: 1121 helix: -0.49 (0.24), residues: 380 sheet: 0.63 (0.29), residues: 275 loop : -0.23 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 82 HIS 0.005 0.001 HIS R 106 PHE 0.016 0.002 PHE B 234 TYR 0.012 0.002 TYR R 146 ARG 0.011 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 1.115 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.2698 time to fit residues: 108.6730 Evaluate side-chains 170 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 0.0970 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 213 HIS A 331 ASN B 220 GLN B 266 HIS B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN C 44 HIS E 179 GLN R 106 HIS R 179 GLN ** R 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9141 Z= 0.298 Angle : 0.747 15.032 12401 Z= 0.378 Chirality : 0.047 0.174 1419 Planarity : 0.005 0.048 1557 Dihedral : 6.536 56.851 1254 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.16 % Allowed : 11.94 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.61 (0.25), residues: 1121 helix: 0.76 (0.26), residues: 385 sheet: 0.78 (0.29), residues: 275 loop : 0.02 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 100 HIS 0.011 0.002 HIS R 393 PHE 0.029 0.002 PHE R 390 TYR 0.020 0.002 TYR B 59 ARG 0.006 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 206 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 225 average time/residue: 0.2431 time to fit residues: 72.8048 Evaluate side-chains 179 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 164 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0860 time to fit residues: 3.7178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 220 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN ** R 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9141 Z= 0.329 Angle : 0.733 14.645 12401 Z= 0.364 Chirality : 0.047 0.237 1419 Planarity : 0.004 0.036 1557 Dihedral : 6.401 55.477 1254 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.67 % Allowed : 13.57 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.51 (0.25), residues: 1121 helix: 0.93 (0.27), residues: 389 sheet: 0.44 (0.28), residues: 299 loop : -0.13 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 100 HIS 0.011 0.001 HIS R 393 PHE 0.021 0.002 PHE R 390 TYR 0.018 0.002 TYR R 34 ARG 0.009 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 184 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 16 residues processed: 208 average time/residue: 0.2482 time to fit residues: 68.6709 Evaluate side-chains 181 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 1.122 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0937 time to fit residues: 4.1922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9141 Z= 0.207 Angle : 0.663 14.594 12401 Z= 0.324 Chirality : 0.045 0.225 1419 Planarity : 0.004 0.055 1557 Dihedral : 6.238 55.892 1254 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.73 % Allowed : 15.82 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.65 (0.26), residues: 1121 helix: 1.17 (0.28), residues: 388 sheet: 0.51 (0.28), residues: 296 loop : -0.17 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 100 HIS 0.002 0.001 HIS A 188 PHE 0.023 0.001 PHE R 389 TYR 0.017 0.001 TYR B 59 ARG 0.013 0.001 ARG R 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 201 average time/residue: 0.2576 time to fit residues: 68.4458 Evaluate side-chains 180 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 169 time to evaluate : 1.038 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1322 time to fit residues: 3.6884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 0.0770 chunk 95 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 244 HIS A 306 GLN B 220 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 393 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9141 Z= 0.169 Angle : 0.632 14.693 12401 Z= 0.307 Chirality : 0.044 0.241 1419 Planarity : 0.003 0.033 1557 Dihedral : 6.052 56.055 1254 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.94 % Allowed : 16.02 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.68 (0.25), residues: 1121 helix: 1.23 (0.28), residues: 388 sheet: 0.45 (0.27), residues: 298 loop : -0.13 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 100 HIS 0.005 0.001 HIS R 393 PHE 0.021 0.001 PHE R 390 TYR 0.013 0.001 TYR R 209 ARG 0.008 0.001 ARG R 220 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 179 time to evaluate : 1.063 Fit side-chains outliers start: 19 outliers final: 7 residues processed: 186 average time/residue: 0.2635 time to fit residues: 65.2532 Evaluate side-chains 171 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 164 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0872 time to fit residues: 2.6834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.6284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9141 Z= 0.194 Angle : 0.645 14.661 12401 Z= 0.313 Chirality : 0.044 0.242 1419 Planarity : 0.003 0.030 1557 Dihedral : 5.939 56.172 1254 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.12 % Allowed : 19.08 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.71 (0.25), residues: 1121 helix: 1.29 (0.28), residues: 387 sheet: 0.56 (0.28), residues: 287 loop : -0.21 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 100 HIS 0.004 0.001 HIS E 232 PHE 0.027 0.001 PHE R 390 TYR 0.010 0.001 TYR B 59 ARG 0.006 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 186 time to evaluate : 1.057 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 191 average time/residue: 0.2549 time to fit residues: 64.2693 Evaluate side-chains 176 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 170 time to evaluate : 1.068 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0902 time to fit residues: 2.3782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 0.0040 chunk 66 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.6511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9141 Z= 0.177 Angle : 0.655 14.893 12401 Z= 0.313 Chirality : 0.044 0.226 1419 Planarity : 0.003 0.028 1557 Dihedral : 5.890 56.839 1254 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.43 % Allowed : 19.39 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.76 (0.25), residues: 1121 helix: 1.29 (0.27), residues: 384 sheet: 0.68 (0.29), residues: 279 loop : -0.18 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 100 HIS 0.003 0.001 HIS B 183 PHE 0.021 0.001 PHE R 389 TYR 0.012 0.001 TYR R 209 ARG 0.007 0.000 ARG R 220 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 188 time to evaluate : 1.142 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 196 average time/residue: 0.2816 time to fit residues: 73.0306 Evaluate side-chains 177 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 170 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0872 time to fit residues: 2.5867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.0127 > 50: distance: 0 - 6: 3.427 distance: 1 - 2: 3.535 distance: 2 - 3: 5.652 distance: 2 - 7: 5.861 distance: 4 - 5: 3.166 distance: 5 - 6: 4.468 distance: 7 - 8: 9.057 distance: 8 - 9: 5.799 distance: 9 - 10: 8.065 distance: 9 - 17: 4.142 distance: 11 - 12: 8.543 distance: 12 - 13: 9.632 distance: 12 - 14: 8.387 distance: 13 - 15: 5.122 distance: 14 - 16: 10.530 distance: 15 - 16: 7.666 distance: 17 - 18: 3.490 distance: 18 - 19: 5.944 distance: 19 - 20: 9.525 distance: 19 - 29: 6.579 distance: 21 - 22: 3.967 distance: 22 - 24: 7.256 distance: 23 - 25: 5.640 distance: 24 - 26: 7.332 distance: 25 - 27: 7.374 distance: 26 - 27: 3.425 distance: 27 - 28: 7.282 distance: 29 - 30: 6.714 distance: 30 - 31: 3.689 distance: 30 - 33: 4.630 distance: 31 - 37: 6.850 distance: 34 - 35: 5.497 distance: 34 - 36: 7.895 distance: 37 - 38: 9.414 distance: 38 - 39: 4.743 distance: 38 - 41: 8.446 distance: 39 - 40: 10.684 distance: 39 - 49: 7.345 distance: 40 - 66: 17.193 distance: 41 - 42: 6.321 distance: 42 - 43: 9.069 distance: 42 - 44: 7.786 distance: 43 - 45: 5.478 distance: 44 - 46: 9.494 distance: 45 - 47: 3.236 distance: 46 - 47: 5.481 distance: 47 - 48: 16.442 distance: 49 - 50: 3.938 distance: 50 - 51: 7.131 distance: 50 - 53: 4.085 distance: 51 - 52: 33.543 distance: 51 - 61: 12.129 distance: 53 - 54: 12.393 distance: 54 - 55: 6.646 distance: 54 - 56: 8.668 distance: 56 - 58: 4.417 distance: 57 - 59: 4.976 distance: 58 - 59: 8.293 distance: 59 - 60: 20.660 distance: 61 - 62: 13.807 distance: 62 - 63: 5.073 distance: 62 - 65: 35.263 distance: 63 - 64: 4.638 distance: 63 - 66: 4.920 distance: 64 - 81: 6.038 distance: 66 - 67: 12.872 distance: 67 - 68: 11.429 distance: 67 - 70: 11.371 distance: 68 - 69: 29.583 distance: 68 - 73: 31.897 distance: 69 - 89: 27.701 distance: 70 - 71: 9.080 distance: 70 - 72: 6.714 distance: 73 - 74: 16.647 distance: 74 - 75: 20.007 distance: 74 - 77: 25.108 distance: 75 - 76: 5.806 distance: 75 - 81: 3.419 distance: 77 - 78: 21.158 distance: 78 - 79: 18.989 distance: 78 - 80: 19.620