Starting phenix.real_space_refine (version: dev) on Mon Dec 12 05:17:51 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbh_31879/12_2022/7vbh_31879_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbh_31879/12_2022/7vbh_31879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbh_31879/12_2022/7vbh_31879.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbh_31879/12_2022/7vbh_31879.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbh_31879/12_2022/7vbh_31879_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbh_31879/12_2022/7vbh_31879_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.089 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 21": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N ARG 105": "NH1" <-> "NH2" Residue "P GLU 16": "OE1" <-> "OE2" Residue "P ARG 17": "NH1" <-> "NH2" Residue "R GLU 34": "OE1" <-> "OE2" Residue "R ARG 40": "NH1" <-> "NH2" Residue "R ARG 43": "NH1" <-> "NH2" Residue "R ARG 44": "NH1" <-> "NH2" Residue "R ARG 121": "NH1" <-> "NH2" Residue "R GLU 125": "OE1" <-> "OE2" Residue "R ARG 326": "NH1" <-> "NH2" Residue "R GLU 364": "OE1" <-> "OE2" Residue "R GLU 373": "OE1" <-> "OE2" Residue "R ARG 376": "NH1" <-> "NH2" Residue "R ARG 414": "NH1" <-> "NH2" Residue "R GLU 418": "OE1" <-> "OE2" Residue "R ARG 421": "NH1" <-> "NH2" Residue "R GLU 423": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 9116 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1761 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 3 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 236 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3105 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 13, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2591 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.89, per 1000 atoms: 0.65 Number of scatterers: 9116 At special positions: 0 Unit cell: (81.396, 96.39, 170.289, 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 53 16.00 O 1669 8.00 N 1577 7.00 C 5817 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.04 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.00 Conformation dependent library (CDL) restraints added in 1.5 seconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2150 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 11 sheets defined 36.7% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.934A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.660A pdb=" N LEU A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 334 through 349 removed outlier: 3.619A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.628A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'P' and resid 4 through 27 Processing helix chain 'R' and resid 32 through 50 Processing helix chain 'R' and resid 139 through 167 Processing helix chain 'R' and resid 175 through 204 Processing helix chain 'R' and resid 207 through 215 Processing helix chain 'R' and resid 220 through 222 No H-bonds generated for 'chain 'R' and resid 220 through 222' Processing helix chain 'R' and resid 224 through 255 removed outlier: 3.965A pdb=" N GLN R 234 " --> pdb=" O PHE R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 290 removed outlier: 3.538A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Proline residue: R 277 - end of helix Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 303 through 335 removed outlier: 4.317A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 360 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 364 No H-bonds generated for 'chain 'R' and resid 362 through 364' Processing helix chain 'R' and resid 378 through 402 removed outlier: 3.892A pdb=" N ILE R 382 " --> pdb=" O THR R 378 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE R 390 " --> pdb=" O THR R 386 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA R 399 " --> pdb=" O GLY R 395 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 421 Processing helix chain 'B' and resid 5 through 23 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'G' and resid 7 through 21 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing sheet with id= A, first strand: chain 'A' and resid 43 through 45 removed outlier: 7.051A pdb=" N ALA A 243 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER A 286 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N PHE A 246 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE A 288 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL A 248 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE A 290 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 208 through 214 Processing sheet with id= C, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.563A pdb=" N LEU N 18 " --> pdb=" O MET N 83 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.554A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.052A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.844A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.753A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 198 through 202 removed outlier: 3.687A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.780A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.507A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.551A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1146 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: 2.62 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1478 1.29 - 1.42: 2571 1.42 - 1.56: 5198 1.56 - 1.69: 3 1.69 - 1.83: 72 Bond restraints: 9322 Sorted by residual: bond pdb=" C02 D6M P 501 " pdb=" C12 D6M P 501 " ideal model delta sigma weight residual 1.517 1.795 -0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" C ASP B 228 " pdb=" O ASP B 228 " ideal model delta sigma weight residual 1.234 1.169 0.064 1.23e-02 6.61e+03 2.75e+01 bond pdb=" C07 D6M P 501 " pdb=" O08 D6M P 501 " ideal model delta sigma weight residual 1.247 1.154 0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C SER B 227 " pdb=" O SER B 227 " ideal model delta sigma weight residual 1.235 1.178 0.057 1.28e-02 6.10e+03 1.97e+01 bond pdb=" N SER B 227 " pdb=" CA SER B 227 " ideal model delta sigma weight residual 1.455 1.394 0.061 1.41e-02 5.03e+03 1.87e+01 ... (remaining 9317 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.82: 248 106.82 - 113.68: 5054 113.68 - 120.55: 3857 120.55 - 127.41: 3360 127.41 - 134.28: 114 Bond angle restraints: 12633 Sorted by residual: angle pdb=" N TYR P 13 " pdb=" CA TYR P 13 " pdb=" C TYR P 13 " ideal model delta sigma weight residual 112.23 100.11 12.12 1.26e+00 6.30e-01 9.25e+01 angle pdb=" C THR P 5 " pdb=" CA THR P 5 " pdb=" CB THR P 5 " ideal model delta sigma weight residual 110.92 100.58 10.34 1.59e+00 3.96e-01 4.23e+01 angle pdb=" N PRO N 100 " pdb=" CA PRO N 100 " pdb=" C PRO N 100 " ideal model delta sigma weight residual 113.47 121.65 -8.18 1.43e+00 4.89e-01 3.28e+01 angle pdb=" N ASP B 228 " pdb=" CA ASP B 228 " pdb=" C ASP B 228 " ideal model delta sigma weight residual 110.42 118.66 -8.24 1.46e+00 4.69e-01 3.18e+01 angle pdb=" CA LYS A 305 " pdb=" CB LYS A 305 " pdb=" CG LYS A 305 " ideal model delta sigma weight residual 114.10 125.33 -11.23 2.00e+00 2.50e-01 3.15e+01 ... (remaining 12628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4864 17.97 - 35.95: 520 35.95 - 53.92: 86 53.92 - 71.90: 27 71.90 - 89.87: 12 Dihedral angle restraints: 5509 sinusoidal: 2185 harmonic: 3324 Sorted by residual: dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual -86.00 -160.71 74.71 1 1.00e+01 1.00e-02 7.07e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 44.87 48.13 1 1.00e+01 1.00e-02 3.19e+01 dihedral pdb=" CA GLU A 327 " pdb=" C GLU A 327 " pdb=" N PRO A 328 " pdb=" CA PRO A 328 " ideal model delta harmonic sigma weight residual 180.00 -151.95 -28.05 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 5506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1154 0.077 - 0.155: 209 0.155 - 0.232: 24 0.232 - 0.310: 2 0.310 - 0.387: 3 Chirality restraints: 1392 Sorted by residual: chirality pdb=" CA ASP B 228 " pdb=" N ASP B 228 " pdb=" C ASP B 228 " pdb=" CB ASP B 228 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CB ILE N 51 " pdb=" CA ILE N 51 " pdb=" CG1 ILE N 51 " pdb=" CG2 ILE N 51 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA PRO N 100 " pdb=" N PRO N 100 " pdb=" C PRO N 100 " pdb=" CB PRO N 100 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 1389 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 D6M P 501 " -0.095 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C04 D6M P 501 " 0.348 2.00e-02 2.50e+03 pdb=" C12 D6M P 501 " 0.123 2.00e-02 2.50e+03 pdb=" N03 D6M P 501 " -0.518 2.00e-02 2.50e+03 pdb=" O01 D6M P 501 " 0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 385 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C PHE R 385 " 0.064 2.00e-02 2.50e+03 pdb=" O PHE R 385 " -0.024 2.00e-02 2.50e+03 pdb=" N THR R 386 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 226 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C GLU B 226 " 0.059 2.00e-02 2.50e+03 pdb=" O GLU B 226 " -0.021 2.00e-02 2.50e+03 pdb=" N SER B 227 " -0.021 2.00e-02 2.50e+03 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 41 2.41 - 3.03: 4894 3.03 - 3.65: 14519 3.65 - 4.28: 22300 4.28 - 4.90: 37240 Nonbonded interactions: 78994 Sorted by model distance: nonbonded pdb=" O LEU P 27 " pdb=" NH2 ARG R 121 " model vdw 1.784 2.520 nonbonded pdb=" CD2 LEU P 26 " pdb=" O GLU R 68 " model vdw 1.908 3.460 nonbonded pdb=" OD1 ASP P 15 " pdb=" N LEU R 32 " model vdw 1.947 2.520 nonbonded pdb=" N HIS P 1 " pdb=" CH2 TRP R 306 " model vdw 1.950 3.420 nonbonded pdb=" O GLY P 29 " pdb=" OE2 GLU R 68 " model vdw 2.182 3.040 ... (remaining 78989 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5817 2.51 5 N 1577 2.21 5 O 1669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.010 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.760 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.090 Process input model: 28.380 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:13.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 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 : 0.010 0.278 9322 Z= 0.674 Angle : 1.117 12.466 12633 Z= 0.621 Chirality : 0.062 0.387 1392 Planarity : 0.011 0.294 1604 Dihedral : 15.865 89.873 3341 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.19), residues: 1117 helix: -2.58 (0.18), residues: 439 sheet: -2.61 (0.29), residues: 212 loop : -2.66 (0.23), residues: 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 163 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 166 average time/residue: 1.0251 time to fit residues: 184.5877 Evaluate side-chains 91 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 1.5519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 0.0980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN P 20 GLN R 302 ASN R 304 ASN R 320 ASN B 9 GLN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 176 GLN B 230 ASN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 59 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 9322 Z= 0.230 Angle : 0.651 8.449 12633 Z= 0.339 Chirality : 0.042 0.150 1392 Planarity : 0.005 0.077 1604 Dihedral : 6.319 56.028 1263 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.85 % Favored : 96.06 % Rotamer Outliers : 3.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.23), residues: 1117 helix: -0.17 (0.24), residues: 439 sheet: -2.01 (0.30), residues: 216 loop : -2.05 (0.26), residues: 462 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 12 residues processed: 156 average time/residue: 0.9262 time to fit residues: 157.9744 Evaluate side-chains 115 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.307 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.7427 time to fit residues: 3.2716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 chunk 27 optimal weight: 0.0870 chunk 100 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.0870 chunk 99 optimal weight: 2.9990 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 263 GLN R 374 HIS R 394 GLN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 9322 Z= 0.168 Angle : 0.556 7.500 12633 Z= 0.294 Chirality : 0.040 0.134 1392 Planarity : 0.004 0.073 1604 Dihedral : 5.827 56.014 1263 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 3.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.24), residues: 1117 helix: 0.96 (0.25), residues: 425 sheet: -1.62 (0.30), residues: 220 loop : -1.78 (0.27), residues: 472 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 114 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 15 residues processed: 144 average time/residue: 0.9118 time to fit residues: 143.5691 Evaluate side-chains 115 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 1.124 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.8943 time to fit residues: 3.4364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 0.1980 chunk 96 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 89 optimal weight: 0.4980 chunk 60 optimal weight: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 20 GLN ** R 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 9322 Z= 0.174 Angle : 0.552 9.682 12633 Z= 0.294 Chirality : 0.041 0.152 1392 Planarity : 0.004 0.073 1604 Dihedral : 5.470 59.103 1263 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.76 % Favored : 96.15 % Rotamer Outliers : 3.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.25), residues: 1117 helix: 1.43 (0.26), residues: 431 sheet: -1.22 (0.32), residues: 216 loop : -1.65 (0.28), residues: 470 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 15 residues processed: 155 average time/residue: 0.9921 time to fit residues: 166.8651 Evaluate side-chains 122 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 1.090 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 6 average time/residue: 0.3969 time to fit residues: 4.3587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 91 optimal weight: 0.0970 chunk 74 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.6544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 9322 Z= 0.301 Angle : 0.662 9.077 12633 Z= 0.347 Chirality : 0.045 0.179 1392 Planarity : 0.005 0.072 1604 Dihedral : 5.684 58.696 1263 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.90 % Rotamer Outliers : 4.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.61 (0.25), residues: 1117 helix: 1.30 (0.25), residues: 430 sheet: -1.18 (0.33), residues: 226 loop : -1.64 (0.28), residues: 461 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 134 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 19 residues processed: 158 average time/residue: 0.9287 time to fit residues: 159.8961 Evaluate side-chains 131 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 13 residues processed: 6 average time/residue: 0.1527 time to fit residues: 3.0045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS R 171 HIS ** R 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 374 HIS B 340 ASN G 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.6861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 9322 Z= 0.201 Angle : 0.586 9.498 12633 Z= 0.303 Chirality : 0.042 0.147 1392 Planarity : 0.004 0.072 1604 Dihedral : 5.279 52.900 1263 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 4.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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 (0.26), residues: 1117 helix: 1.57 (0.25), residues: 436 sheet: -0.83 (0.34), residues: 219 loop : -1.56 (0.28), residues: 462 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 117 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 29 residues processed: 143 average time/residue: 0.9904 time to fit residues: 154.0449 Evaluate side-chains 137 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 108 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 16 residues processed: 13 average time/residue: 0.4562 time to fit residues: 8.3796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 66 optimal weight: 0.0570 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 20.0000 chunk 63 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 171 HIS ** R 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.7097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 9322 Z= 0.185 Angle : 0.571 8.406 12633 Z= 0.296 Chirality : 0.041 0.144 1392 Planarity : 0.004 0.071 1604 Dihedral : 5.130 52.433 1263 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 4.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.26), residues: 1117 helix: 1.80 (0.25), residues: 436 sheet: -0.75 (0.34), residues: 219 loop : -1.53 (0.28), residues: 462 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 119 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 25 residues processed: 144 average time/residue: 1.0068 time to fit residues: 157.3821 Evaluate side-chains 138 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 1.032 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 18 residues processed: 7 average time/residue: 0.1724 time to fit residues: 3.2135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 171 HIS ** R 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.7344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 9322 Z= 0.208 Angle : 0.596 7.859 12633 Z= 0.308 Chirality : 0.042 0.150 1392 Planarity : 0.004 0.071 1604 Dihedral : 5.135 52.292 1263 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 3.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.26), residues: 1117 helix: 1.94 (0.25), residues: 431 sheet: -0.66 (0.35), residues: 220 loop : -1.51 (0.28), residues: 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 116 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 27 residues processed: 140 average time/residue: 0.9404 time to fit residues: 143.6947 Evaluate side-chains 141 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 19 residues processed: 8 average time/residue: 0.4638 time to fit residues: 5.7633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 105 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 5 GLN R 171 HIS ** R 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.7515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 9322 Z= 0.181 Angle : 0.585 8.606 12633 Z= 0.301 Chirality : 0.041 0.146 1392 Planarity : 0.004 0.070 1604 Dihedral : 5.000 51.855 1263 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 3.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 1117 helix: 2.09 (0.25), residues: 428 sheet: -0.58 (0.35), residues: 220 loop : -1.47 (0.28), residues: 469 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 24 residues processed: 138 average time/residue: 0.9512 time to fit residues: 143.4777 Evaluate side-chains 131 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 1.127 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 19 residues processed: 5 average time/residue: 0.1500 time to fit residues: 2.6809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 101 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 171 HIS ** R 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.7678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 9322 Z= 0.288 Angle : 0.644 7.645 12633 Z= 0.335 Chirality : 0.043 0.164 1392 Planarity : 0.004 0.068 1604 Dihedral : 5.258 53.372 1263 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1117 helix: 1.80 (0.25), residues: 437 sheet: -0.68 (0.34), residues: 220 loop : -1.52 (0.28), residues: 460 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 113 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 23 residues processed: 135 average time/residue: 0.9498 time to fit residues: 140.0769 Evaluate side-chains 135 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 0.0966 time to fit residues: 2.0003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 90 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 HIS ** R 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.195433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.155634 restraints weight = 10317.128| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.64 r_work: 0.3560 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.7831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 9322 Z= 0.204 Angle : 0.603 8.888 12633 Z= 0.312 Chirality : 0.042 0.158 1392 Planarity : 0.004 0.068 1604 Dihedral : 5.091 51.648 1263 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.26), residues: 1117 helix: 2.07 (0.25), residues: 429 sheet: -0.60 (0.34), residues: 220 loop : -1.42 (0.28), residues: 468 =============================================================================== Job complete usr+sys time: 3276.58 seconds wall clock time: 59 minutes 6.78 seconds (3546.78 seconds total)