Starting phenix.real_space_refine on Fri Dec 8 15:57:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvl_32143/12_2023/7vvl_32143.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvl_32143/12_2023/7vvl_32143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvl_32143/12_2023/7vvl_32143.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvl_32143/12_2023/7vvl_32143.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvl_32143/12_2023/7vvl_32143.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvl_32143/12_2023/7vvl_32143.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5546 2.51 5 N 1523 2.21 5 O 1603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "P GLU 22": "OE1" <-> "OE2" Residue "R GLU 36": "OE1" <-> "OE2" Residue "R TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 137": "OD1" <-> "OD2" Residue "R TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 431": "OE1" <-> "OE2" 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: 8725 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1901 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2519 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "G" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 392 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 968 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 280 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 33} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE%COO:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2665 Classifications: {'peptide': 346, 'water': 1} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 9, 'TRANS': 336, None: 1} Not linked: pdbres="TRP R 477 " pdbres="HOH R 501 " Chain breaks: 4 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 283 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 4, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 152 Time building chain proxies: 5.06, per 1000 atoms: 0.58 Number of scatterers: 8725 At special positions: 0 Unit cell: (128.374, 99.6003, 127.267, 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 1603 8.00 N 1523 7.00 C 5546 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.07 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.02 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: 3.37 Conformation dependent library (CDL) restraints added in 1.7 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 41.8% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.787A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.520A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.632A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.568A pdb=" N LEU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.163A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.537A pdb=" N TYR A 308 " --> pdb=" O PHE A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.540A pdb=" N ARG A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 381 removed outlier: 3.511A pdb=" N ILE A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 11 through 24 removed outlier: 3.800A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.835A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 34 Processing helix chain 'R' and resid 33 through 49 Processing helix chain 'R' and resid 179 through 212 removed outlier: 4.196A pdb=" N VAL R 183 " --> pdb=" O ARG R 179 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR R 211 " --> pdb=" O LEU R 207 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 Processing helix chain 'R' and resid 217 through 245 removed outlier: 3.555A pdb=" N ILE R 222 " --> pdb=" O THR R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 312 removed outlier: 3.545A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR R 286 " --> pdb=" O ARG R 282 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 344 removed outlier: 3.541A pdb=" N THR R 325 " --> pdb=" O LEU R 321 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.648A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 359 removed outlier: 4.090A pdb=" N LYS R 359 " --> pdb=" O SER R 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 356 through 359' Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix removed outlier: 3.503A pdb=" N ASN R 374 " --> pdb=" O SER R 370 " (cutoff:3.500A) Processing helix chain 'R' and resid 398 through 400 No H-bonds generated for 'chain 'R' and resid 398 through 400' Processing helix chain 'R' and resid 401 through 413 removed outlier: 3.756A pdb=" N LEU R 406 " --> pdb=" O GLN R 402 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU R 407 " --> pdb=" O TYR R 403 " (cutoff:3.500A) Processing helix chain 'R' and resid 413 through 418 Processing helix chain 'R' and resid 419 through 423 removed outlier: 3.702A pdb=" N VAL R 423 " --> pdb=" O HIS R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 461 removed outlier: 3.531A pdb=" N PHE R 450 " --> pdb=" O LEU R 446 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 477 removed outlier: 3.692A pdb=" N LYS R 472 " --> pdb=" O ALA R 468 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER R 473 " --> pdb=" O GLU R 469 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.984A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.812A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.800A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.735A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.935A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.020A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.373A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.617A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.520A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 111 through 112 removed outlier: 3.639A pdb=" N GLU R 111 " --> pdb=" O TRP R 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 128 through 130 453 hydrogen bonds defined for protein. 1290 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: 2.43 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1424 1.30 - 1.43: 2492 1.43 - 1.56: 4915 1.56 - 1.69: 1 1.69 - 1.83: 78 Bond restraints: 8910 Sorted by residual: bond pdb=" CE1 HIS R 307 " pdb=" NE2 HIS R 307 " ideal model delta sigma weight residual 1.321 1.374 -0.053 1.00e-02 1.00e+04 2.79e+01 bond pdb=" C ARG R 150 " pdb=" O ARG R 150 " ideal model delta sigma weight residual 1.236 1.301 -0.064 1.26e-02 6.30e+03 2.61e+01 bond pdb=" C PRO A 351 " pdb=" O PRO A 351 " ideal model delta sigma weight residual 1.233 1.180 0.053 1.10e-02 8.26e+03 2.36e+01 bond pdb=" C ASN R 139 " pdb=" O ASN R 139 " ideal model delta sigma weight residual 1.234 1.171 0.063 1.35e-02 5.49e+03 2.18e+01 bond pdb=" N VAL R 157 " pdb=" CA VAL R 157 " ideal model delta sigma weight residual 1.460 1.494 -0.034 7.50e-03 1.78e+04 2.11e+01 ... (remaining 8905 not shown) Histogram of bond angle deviations from ideal: 97.65 - 105.12: 119 105.12 - 112.59: 4218 112.59 - 120.06: 4269 120.06 - 127.53: 3385 127.53 - 135.00: 99 Bond angle restraints: 12090 Sorted by residual: angle pdb=" N PRO N 102 " pdb=" CA PRO N 102 " pdb=" C PRO N 102 " ideal model delta sigma weight residual 114.35 121.98 -7.63 1.25e+00 6.40e-01 3.72e+01 angle pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" O VAL A 224 " ideal model delta sigma weight residual 122.63 118.12 4.51 8.70e-01 1.32e+00 2.69e+01 angle pdb=" N GLU P 4 " pdb=" CA GLU P 4 " pdb=" C GLU P 4 " ideal model delta sigma weight residual 111.14 105.80 5.34 1.08e+00 8.57e-01 2.44e+01 angle pdb=" C GLU B 130 " pdb=" N GLY B 131 " pdb=" CA GLY B 131 " ideal model delta sigma weight residual 119.94 125.41 -5.47 1.11e+00 8.12e-01 2.43e+01 angle pdb=" CB GLU A 312 " pdb=" CG GLU A 312 " pdb=" CD GLU A 312 " ideal model delta sigma weight residual 112.60 120.46 -7.86 1.70e+00 3.46e-01 2.14e+01 ... (remaining 12085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 4523 17.64 - 35.27: 513 35.27 - 52.90: 167 52.90 - 70.54: 34 70.54 - 88.17: 18 Dihedral angle restraints: 5255 sinusoidal: 1978 harmonic: 3277 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -146.52 60.52 1 1.00e+01 1.00e-02 4.88e+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 49.34 43.66 1 1.00e+01 1.00e-02 2.65e+01 dihedral pdb=" CA THR A 359 " pdb=" C THR A 359 " pdb=" N GLU A 360 " pdb=" CA GLU A 360 " ideal model delta harmonic sigma weight residual 180.00 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 5252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 752 0.068 - 0.136: 443 0.136 - 0.204: 138 0.204 - 0.272: 24 0.272 - 0.340: 4 Chirality restraints: 1361 Sorted by residual: chirality pdb=" CA PRO N 102 " pdb=" N PRO N 102 " pdb=" C PRO N 102 " pdb=" CB PRO N 102 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB ILE R 135 " pdb=" CA ILE R 135 " pdb=" CG1 ILE R 135 " pdb=" CG2 ILE R 135 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA LEU B 318 " pdb=" N LEU B 318 " pdb=" C LEU B 318 " pdb=" CB LEU B 318 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 1358 not shown) Planarity restraints: 1545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 329 " -0.017 2.00e-02 2.50e+03 8.90e-03 1.98e+00 pdb=" CG TRP R 329 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP R 329 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP R 329 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP R 329 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 329 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP R 329 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 329 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 329 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP R 329 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 271 " 0.019 2.00e-02 2.50e+03 8.80e-03 1.94e+00 pdb=" CG TRP A 271 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TRP A 271 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 271 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 271 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 271 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 271 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 271 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 271 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 271 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 134 " 0.004 2.00e-02 2.50e+03 8.46e-03 1.43e+00 pdb=" CG TYR R 134 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR R 134 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR R 134 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR R 134 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR R 134 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR R 134 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR R 134 " 0.001 2.00e-02 2.50e+03 ... (remaining 1542 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 561 2.74 - 3.28: 8583 3.28 - 3.82: 14112 3.82 - 4.36: 19286 4.36 - 4.90: 31185 Nonbonded interactions: 73727 Sorted by model distance: nonbonded pdb=" O SER R 356 " pdb=" OG SER R 356 " model vdw 2.204 2.440 nonbonded pdb=" O GLN R 438 " pdb=" ND1 HIS R 442 " model vdw 2.262 2.520 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.265 2.520 nonbonded pdb=" OG1 THR N 28 " pdb=" ND2 ASN N 31 " model vdw 2.289 2.520 nonbonded pdb=" NH1 ARG R 282 " pdb=" OD1 ASN R 348 " model vdw 2.303 2.520 ... (remaining 73722 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 1.080 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.070 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.014 0.066 8910 Z= 0.932 Angle : 1.688 9.035 12090 Z= 1.233 Chirality : 0.089 0.340 1361 Planarity : 0.003 0.012 1545 Dihedral : 17.696 88.173 3126 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.26 % Favored : 95.65 % Rotamer: Outliers : 7.24 % Allowed : 19.15 % Favored : 73.61 % 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: -0.88 (0.24), residues: 1104 helix: -0.35 (0.23), residues: 426 sheet: 0.15 (0.37), residues: 206 loop : -1.03 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP A 271 HIS 0.006 0.001 HIS B 311 PHE 0.012 0.003 PHE R 378 TYR 0.016 0.003 TYR R 134 ARG 0.005 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 164 time to evaluate : 1.021 Fit side-chains outliers start: 65 outliers final: 23 residues processed: 214 average time/residue: 1.2169 time to fit residues: 276.7298 Evaluate side-chains 154 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 0.892 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 19 residues processed: 4 average time/residue: 0.5430 time to fit residues: 3.6615 ------------------------------------------------------------------------------- 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: 0.7980 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 259 GLN B 340 ASN G 44 HIS G 59 ASN N 31 ASN P 16 ASN ** R 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 374 ASN R 402 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8910 Z= 0.271 Angle : 0.584 6.757 12090 Z= 0.321 Chirality : 0.044 0.160 1361 Planarity : 0.004 0.046 1545 Dihedral : 4.550 22.656 1223 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 6.35 % Allowed : 22.83 % Favored : 70.82 % 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: 0.16 (0.25), residues: 1104 helix: 1.15 (0.24), residues: 444 sheet: -0.27 (0.34), residues: 222 loop : -0.69 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.004 0.001 HIS A 347 PHE 0.018 0.002 PHE A 212 TYR 0.023 0.002 TYR R 191 ARG 0.006 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 138 time to evaluate : 1.092 Fit side-chains revert: symmetry clash outliers start: 57 outliers final: 33 residues processed: 180 average time/residue: 1.1484 time to fit residues: 221.3374 Evaluate side-chains 153 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 120 time to evaluate : 0.882 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 24 residues processed: 9 average time/residue: 0.3071 time to fit residues: 4.7272 ------------------------------------------------------------------------------- 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: 7.9990 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 0.0040 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 108 optimal weight: 0.0870 chunk 89 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.6174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 44 HIS P 16 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8910 Z= 0.192 Angle : 0.504 6.474 12090 Z= 0.276 Chirality : 0.041 0.145 1361 Planarity : 0.004 0.051 1545 Dihedral : 4.219 24.436 1223 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 6.57 % Allowed : 22.61 % Favored : 70.82 % 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: 0.58 (0.25), residues: 1104 helix: 1.77 (0.25), residues: 444 sheet: -0.19 (0.32), residues: 219 loop : -0.70 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.016 0.001 PHE A 212 TYR 0.023 0.001 TYR R 191 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 136 time to evaluate : 0.962 Fit side-chains revert: symmetry clash outliers start: 59 outliers final: 35 residues processed: 182 average time/residue: 1.2067 time to fit residues: 234.3427 Evaluate side-chains 161 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 0.997 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 28 residues processed: 7 average time/residue: 0.4158 time to fit residues: 4.7063 ------------------------------------------------------------------------------- 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: 8.9990 chunk 75 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 0.0770 chunk 28 optimal weight: 3.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 44 HIS P 16 ASN R 223 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8910 Z= 0.182 Angle : 0.490 7.020 12090 Z= 0.268 Chirality : 0.041 0.144 1361 Planarity : 0.004 0.053 1545 Dihedral : 4.125 25.769 1223 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 7.13 % Allowed : 23.39 % Favored : 69.49 % 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: 0.72 (0.26), residues: 1104 helix: 2.03 (0.25), residues: 438 sheet: -0.21 (0.33), residues: 219 loop : -0.69 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.016 0.001 PHE R 335 TYR 0.022 0.002 TYR R 191 ARG 0.003 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 135 time to evaluate : 0.998 Fit side-chains revert: symmetry clash outliers start: 64 outliers final: 42 residues processed: 181 average time/residue: 1.2778 time to fit residues: 245.9516 Evaluate side-chains 170 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 128 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 32 residues processed: 10 average time/residue: 0.3705 time to fit residues: 5.8151 ------------------------------------------------------------------------------- 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: 9.9990 chunk 60 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN B 142 HIS B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 11 GLN G 44 HIS P 16 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 8910 Z= 0.579 Angle : 0.742 9.885 12090 Z= 0.397 Chirality : 0.052 0.219 1361 Planarity : 0.006 0.059 1545 Dihedral : 5.163 35.469 1223 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 8.57 % Allowed : 23.27 % Favored : 68.15 % 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: -0.26 (0.25), residues: 1104 helix: 0.94 (0.24), residues: 439 sheet: -0.63 (0.32), residues: 229 loop : -0.98 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 82 HIS 0.006 0.002 HIS R 420 PHE 0.019 0.003 PHE R 335 TYR 0.022 0.003 TYR R 191 ARG 0.006 0.001 ARG R 179 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 133 time to evaluate : 1.045 Fit side-chains outliers start: 77 outliers final: 49 residues processed: 194 average time/residue: 1.1718 time to fit residues: 242.8526 Evaluate side-chains 174 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 125 time to evaluate : 1.047 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 43 residues processed: 6 average time/residue: 0.2714 time to fit residues: 3.4291 ------------------------------------------------------------------------------- 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: 0.2980 chunk 95 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 26 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 176 GLN B 237 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS P 16 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8910 Z= 0.144 Angle : 0.477 7.423 12090 Z= 0.263 Chirality : 0.040 0.140 1361 Planarity : 0.004 0.056 1545 Dihedral : 4.261 30.710 1223 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 6.01 % Allowed : 25.39 % Favored : 68.60 % 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: 0.51 (0.25), residues: 1104 helix: 1.86 (0.25), residues: 438 sheet: -0.31 (0.33), residues: 217 loop : -0.81 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 211 HIS 0.006 0.001 HIS A 220 PHE 0.018 0.001 PHE R 335 TYR 0.022 0.001 TYR R 191 ARG 0.003 0.000 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 137 time to evaluate : 1.043 Fit side-chains outliers start: 54 outliers final: 41 residues processed: 184 average time/residue: 1.2055 time to fit residues: 237.6909 Evaluate side-chains 171 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 130 time to evaluate : 0.904 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 36 residues processed: 5 average time/residue: 0.2721 time to fit residues: 2.9803 ------------------------------------------------------------------------------- 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: 7.9990 chunk 60 optimal weight: 0.0050 chunk 77 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 59 optimal weight: 0.0980 chunk 106 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN B 142 HIS B 176 GLN B 340 ASN G 44 HIS P 16 ASN R 216 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8910 Z= 0.153 Angle : 0.484 8.682 12090 Z= 0.264 Chirality : 0.040 0.139 1361 Planarity : 0.004 0.056 1545 Dihedral : 4.081 26.549 1223 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.90 % Allowed : 25.84 % Favored : 68.26 % 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: 0.72 (0.26), residues: 1104 helix: 2.14 (0.26), residues: 438 sheet: -0.29 (0.33), residues: 215 loop : -0.78 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.016 0.001 PHE R 335 TYR 0.021 0.001 TYR R 191 ARG 0.003 0.000 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 135 time to evaluate : 0.994 Fit side-chains outliers start: 53 outliers final: 41 residues processed: 180 average time/residue: 1.2010 time to fit residues: 230.8688 Evaluate side-chains 173 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 132 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 36 residues processed: 5 average time/residue: 0.4794 time to fit residues: 4.0177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 67 optimal weight: 0.4980 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 83 optimal weight: 30.0000 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN B 142 HIS B 176 GLN B 340 ASN P 16 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8910 Z= 0.171 Angle : 0.494 9.558 12090 Z= 0.268 Chirality : 0.040 0.139 1361 Planarity : 0.004 0.057 1545 Dihedral : 4.058 25.049 1223 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.68 % Allowed : 26.50 % Favored : 67.82 % 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: 0.79 (0.26), residues: 1104 helix: 2.23 (0.26), residues: 433 sheet: -0.35 (0.33), residues: 218 loop : -0.68 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.016 0.001 PHE R 335 TYR 0.020 0.001 TYR R 191 ARG 0.003 0.000 ARG R 179 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 128 time to evaluate : 0.901 Fit side-chains outliers start: 51 outliers final: 42 residues processed: 170 average time/residue: 1.2049 time to fit residues: 218.9620 Evaluate side-chains 168 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 126 time to evaluate : 0.987 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 38 residues processed: 4 average time/residue: 0.6020 time to fit residues: 4.0958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 176 GLN B 340 ASN P 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8910 Z= 0.144 Angle : 0.474 10.671 12090 Z= 0.257 Chirality : 0.040 0.134 1361 Planarity : 0.004 0.056 1545 Dihedral : 3.903 22.049 1223 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.35 % Allowed : 26.73 % Favored : 67.93 % 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: 0.95 (0.26), residues: 1104 helix: 2.39 (0.26), residues: 432 sheet: -0.25 (0.33), residues: 215 loop : -0.64 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.016 0.001 PHE R 335 TYR 0.020 0.001 TYR R 191 ARG 0.004 0.000 ARG R 383 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 132 time to evaluate : 1.092 Fit side-chains outliers start: 48 outliers final: 39 residues processed: 174 average time/residue: 1.1966 time to fit residues: 222.3995 Evaluate side-chains 167 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 128 time to evaluate : 0.993 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 36 residues processed: 3 average time/residue: 0.0903 time to fit residues: 1.9072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 176 GLN B 340 ASN P 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8910 Z= 0.199 Angle : 0.518 11.541 12090 Z= 0.277 Chirality : 0.041 0.146 1361 Planarity : 0.004 0.055 1545 Dihedral : 4.077 24.638 1223 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.57 % Allowed : 27.84 % Favored : 67.59 % 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: 0.81 (0.26), residues: 1104 helix: 2.24 (0.25), residues: 433 sheet: -0.33 (0.33), residues: 217 loop : -0.67 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.016 0.001 PHE R 230 TYR 0.021 0.002 TYR R 191 ARG 0.004 0.000 ARG R 383 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 127 time to evaluate : 0.957 Fit side-chains outliers start: 41 outliers final: 37 residues processed: 166 average time/residue: 1.2069 time to fit residues: 213.6203 Evaluate side-chains 163 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 126 time to evaluate : 0.982 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 36 residues processed: 1 average time/residue: 0.0778 time to fit residues: 1.5447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 340 ASN P 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.150927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.114378 restraints weight = 10360.474| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.05 r_work: 0.3177 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8910 Z= 0.356 Angle : 0.609 11.716 12090 Z= 0.325 Chirality : 0.046 0.166 1361 Planarity : 0.005 0.058 1545 Dihedral : 4.566 30.360 1223 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.12 % Allowed : 27.73 % Favored : 67.15 % 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: 0.40 (0.25), residues: 1104 helix: 1.73 (0.25), residues: 439 sheet: -0.43 (0.32), residues: 224 loop : -0.82 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.007 0.002 HIS A 220 PHE 0.016 0.002 PHE A 212 TYR 0.023 0.002 TYR R 191 ARG 0.005 0.001 ARG R 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4059.76 seconds wall clock time: 72 minutes 23.51 seconds (4343.51 seconds total)